Mercury in PDB 4q2e: Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
Enzymatic activity of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
All present enzymatic activity of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant):
2.7.7.41;
Protein crystallography data
The structure of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant), PDB code: 4q2e
was solved by
X.Liu,
Y.Yin,
J.Wu,
Z.Liu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.00 /
3.40
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
142.080,
142.080,
198.373,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
29.9 /
33.8
|
Other elements in 4q2e:
The structure of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) also contains other interesting chemical elements:
Mercury Binding Sites:
The binding sites of Mercury atom in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
(pdb code 4q2e). This binding sites where shown within
5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the
Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant), PDB code: 4q2e:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
Mercury binding site 1 out
of 6 in 4q2e
Go back to
Mercury Binding Sites List in 4q2e
Mercury binding site 1 out
of 6 in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
 Mono view
 Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 1 of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg301
b:0.3
occ:1.00
|
SG
|
A:CYS220
|
2.1
|
0.3
|
1.0
|
CB
|
A:CYS220
|
3.2
|
0.1
|
1.0
|
CA
|
A:CYS220
|
3.9
|
0.8
|
1.0
|
NH2
|
A:ARG207
|
4.2
|
0.0
|
1.0
|
CE2
|
A:PHE221
|
4.5
|
0.3
|
1.0
|
CD2
|
A:PHE221
|
4.6
|
0.7
|
1.0
|
N
|
A:PHE221
|
4.7
|
0.5
|
1.0
|
C
|
A:CYS220
|
4.8
|
0.5
|
1.0
|
N
|
A:CYS220
|
4.9
|
0.4
|
1.0
|
OE2
|
A:GLU286
|
5.0
|
0.1
|
1.0
|
|
Mercury binding site 2 out
of 6 in 4q2e
Go back to
Mercury Binding Sites List in 4q2e
Mercury binding site 2 out
of 6 in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
 Mono view
 Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 2 of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg302
b:0.7
occ:1.00
|
SG
|
A:CYS41
|
2.1
|
0.7
|
1.0
|
O
|
A:PHE37
|
2.7
|
0.3
|
1.0
|
CB
|
A:CYS41
|
3.3
|
0.7
|
1.0
|
N
|
A:CYS41
|
3.4
|
0.1
|
1.0
|
CA
|
A:CYS41
|
3.6
|
0.5
|
1.0
|
C
|
A:PHE37
|
3.6
|
0.3
|
1.0
|
CE2
|
A:PHE37
|
3.7
|
0.6
|
1.0
|
CD2
|
A:PHE37
|
3.7
|
0.8
|
1.0
|
CZ
|
A:PHE37
|
3.8
|
0.2
|
1.0
|
C
|
A:LEU40
|
3.9
|
0.7
|
1.0
|
CG
|
A:PHE37
|
3.9
|
0.6
|
1.0
|
CE1
|
A:PHE37
|
3.9
|
0.1
|
1.0
|
CD1
|
A:PHE37
|
4.0
|
0.0
|
1.0
|
CB
|
A:LEU40
|
4.2
|
0.1
|
1.0
|
CA
|
A:PHE37
|
4.3
|
0.7
|
1.0
|
O
|
A:LEU40
|
4.4
|
0.3
|
1.0
|
CA
|
A:LEU40
|
4.5
|
0.3
|
1.0
|
N
|
A:VAL38
|
4.6
|
0.9
|
1.0
|
CG
|
A:LEU40
|
4.7
|
0.4
|
1.0
|
CB
|
A:PHE37
|
4.7
|
0.8
|
1.0
|
O
|
A:VAL38
|
4.7
|
0.9
|
1.0
|
N
|
A:LEU40
|
4.8
|
0.9
|
1.0
|
CA
|
A:VAL38
|
5.0
|
0.8
|
1.0
|
C
|
A:VAL38
|
5.0
|
0.7
|
1.0
|
|
Mercury binding site 3 out
of 6 in 4q2e
Go back to
Mercury Binding Sites List in 4q2e
Mercury binding site 3 out
of 6 in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
 Mono view
 Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 3 of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Hg303
b:0.2
occ:1.00
|
SG
|
A:CYS243
|
2.1
|
0.6
|
1.0
|
CB
|
A:CYS243
|
3.0
|
0.9
|
1.0
|
O
|
A:TYR183
|
3.3
|
0.0
|
1.0
|
CA
|
A:CYS243
|
3.4
|
0.6
|
1.0
|
O
|
A:CYS243
|
3.5
|
0.2
|
1.0
|
CE
|
A:LYS246
|
3.5
|
0.3
|
1.0
|
CG
|
A:ARG247
|
3.6
|
0.4
|
1.0
|
NE
|
A:ARG247
|
3.8
|
0.8
|
1.0
|
C
|
A:CYS243
|
3.8
|
0.4
|
1.0
|
NZ
|
A:LYS246
|
3.9
|
0.2
|
1.0
|
CZ
|
A:ARG247
|
3.9
|
0.6
|
1.0
|
NH2
|
A:ARG247
|
4.2
|
0.8
|
1.0
|
CD
|
A:ARG247
|
4.2
|
0.6
|
1.0
|
C
|
A:TYR183
|
4.3
|
0.7
|
1.0
|
NH1
|
A:ARG247
|
4.4
|
0.8
|
1.0
|
CA
|
A:SER184
|
4.4
|
0.2
|
1.0
|
CB
|
A:LYS246
|
4.4
|
0.1
|
1.0
|
N
|
A:ARG247
|
4.7
|
0.8
|
1.0
|
N
|
A:CYS243
|
4.8
|
98.5
|
1.0
|
CD
|
A:LYS246
|
4.8
|
0.6
|
1.0
|
C
|
A:SER184
|
4.8
|
0.2
|
1.0
|
CB
|
A:ARG247
|
4.8
|
0.4
|
1.0
|
CD
|
A:PRO185
|
4.8
|
0.9
|
1.0
|
N
|
A:SER184
|
4.8
|
0.8
|
1.0
|
N
|
A:PRO185
|
4.9
|
0.5
|
1.0
|
|
Mercury binding site 4 out
of 6 in 4q2e
Go back to
Mercury Binding Sites List in 4q2e
Mercury binding site 4 out
of 6 in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
 Mono view
 Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 4 of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg301
b:1.0
occ:1.00
|
SG
|
B:CYS220
|
2.1
|
0.7
|
1.0
|
CB
|
B:CYS220
|
3.1
|
0.2
|
1.0
|
CA
|
B:CYS220
|
3.6
|
0.7
|
1.0
|
NH2
|
B:ARG207
|
3.9
|
0.7
|
1.0
|
CD2
|
B:PHE221
|
4.4
|
0.5
|
1.0
|
CE2
|
B:PHE221
|
4.4
|
0.7
|
1.0
|
N
|
B:PHE221
|
4.5
|
0.6
|
1.0
|
C
|
B:CYS220
|
4.6
|
0.6
|
1.0
|
N
|
B:CYS220
|
4.7
|
0.9
|
1.0
|
CZ
|
B:ARG207
|
4.8
|
0.9
|
1.0
|
OE2
|
B:GLU286
|
5.0
|
0.7
|
1.0
|
|
Mercury binding site 5 out
of 6 in 4q2e
Go back to
Mercury Binding Sites List in 4q2e
Mercury binding site 5 out
of 6 in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
 Mono view
 Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 5 of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg302
b:0.6
occ:1.00
|
SG
|
B:CYS41
|
2.1
|
0.5
|
1.0
|
O
|
B:PHE37
|
2.7
|
0.6
|
1.0
|
CE2
|
B:PHE37
|
3.4
|
0.6
|
1.0
|
CD2
|
B:PHE37
|
3.4
|
0.2
|
1.0
|
CZ
|
B:PHE37
|
3.5
|
0.9
|
1.0
|
CB
|
B:CYS41
|
3.5
|
0.5
|
1.0
|
C
|
B:PHE37
|
3.6
|
0.3
|
1.0
|
CG
|
B:PHE37
|
3.6
|
0.7
|
1.0
|
N
|
B:CYS41
|
3.6
|
0.2
|
1.0
|
CE1
|
B:PHE37
|
3.7
|
0.8
|
1.0
|
CD1
|
B:PHE37
|
3.7
|
0.3
|
1.0
|
CA
|
B:CYS41
|
3.8
|
0.2
|
1.0
|
CA
|
B:PHE37
|
4.1
|
0.5
|
1.0
|
C
|
B:LEU40
|
4.2
|
0.0
|
1.0
|
CB
|
B:LEU40
|
4.3
|
0.6
|
1.0
|
CB
|
B:PHE37
|
4.5
|
0.9
|
1.0
|
N
|
B:VAL38
|
4.6
|
0.7
|
1.0
|
CA
|
B:LEU40
|
4.7
|
0.3
|
1.0
|
O
|
B:LEU40
|
4.7
|
0.9
|
1.0
|
CG
|
B:LEU40
|
4.8
|
0.8
|
1.0
|
O
|
B:VAL38
|
4.8
|
0.8
|
1.0
|
CA
|
B:VAL38
|
5.0
|
0.1
|
1.0
|
N
|
B:LEU40
|
5.0
|
1.0
|
1.0
|
|
Mercury binding site 6 out
of 6 in 4q2e
Go back to
Mercury Binding Sites List in 4q2e
Mercury binding site 6 out
of 6 in the Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant)
 Mono view
 Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg binding
site number 6 of Crystal Structure of An Intramembrane Cdp-Dag Synthetase Central For Phospholipid Biosynthesis (S200C/S258C, Active Mutant) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Hg303
b:0.8
occ:1.00
|
SG
|
B:CYS243
|
2.1
|
0.6
|
1.0
|
O
|
B:TYR183
|
3.0
|
0.9
|
1.0
|
CE
|
B:LYS246
|
3.1
|
0.0
|
1.0
|
CB
|
B:CYS243
|
3.2
|
0.3
|
1.0
|
NZ
|
B:LYS246
|
3.4
|
0.2
|
1.0
|
CA
|
B:CYS243
|
3.5
|
0.5
|
1.0
|
O
|
B:CYS243
|
3.7
|
0.7
|
1.0
|
CZ
|
B:ARG247
|
4.0
|
0.3
|
1.0
|
CG
|
B:ARG247
|
4.0
|
0.5
|
1.0
|
C
|
B:CYS243
|
4.1
|
0.5
|
1.0
|
NE
|
B:ARG247
|
4.1
|
0.3
|
1.0
|
C
|
B:TYR183
|
4.1
|
0.1
|
1.0
|
CB
|
B:LYS246
|
4.2
|
0.0
|
1.0
|
NH2
|
B:ARG247
|
4.3
|
0.1
|
1.0
|
NH1
|
B:ARG247
|
4.3
|
0.6
|
1.0
|
CD
|
B:LYS246
|
4.4
|
0.6
|
1.0
|
CA
|
B:SER184
|
4.5
|
0.3
|
1.0
|
O
|
B:LYS252
|
4.5
|
0.6
|
1.0
|
CD
|
B:ARG247
|
4.6
|
0.5
|
1.0
|
N
|
B:SER184
|
4.7
|
0.9
|
1.0
|
N
|
B:CYS243
|
4.8
|
99.7
|
1.0
|
N
|
B:ARG247
|
4.8
|
0.3
|
1.0
|
O
|
B:VAL251
|
4.9
|
0.2
|
1.0
|
CG
|
B:LYS246
|
4.9
|
0.2
|
1.0
|
C
|
B:SER184
|
4.9
|
0.8
|
1.0
|
|
Reference:
X.Liu,
Y.Yin,
J.Wu,
Z.Liu.
Structure and Mechanism of An Intramembrane Liponucleotide Synthetase Central For Phospholipid Biosynthesis Nat Commun V. 5 4244 2014.
ISSN: ESSN 2041-1723
PubMed: 24968740
DOI: 10.1038/NCOMMS5244
Page generated: Sun Aug 11 05:07:49 2024
|