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Mercury in PDB 2epm: N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii

Enzymatic activity of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii

All present enzymatic activity of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii:
3.2.1.52;

Protein crystallography data

The structure of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii, PDB code: 2epm was solved by D.B.Langley, D.W.S.Harty, J.M.Guss, C.A.Collyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.95 / 2.04
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 122.964, 124.746, 147.889, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.7

Mercury Binding Sites:

The binding sites of Mercury atom in the N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii (pdb code 2epm). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 6 binding sites of Mercury where determined in the N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii, PDB code: 2epm:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6;

Mercury binding site 1 out of 6 in 2epm

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Mercury binding site 1 out of 6 in the N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg630

b:48.5
occ:0.70
 SG X:CYS361 2.0 42.6 1.0
O X:ALA357 2.9 38.8 1.0
N X:CYS361 3.3 48.1 1.0
CB X:CYS361 3.3 44.5 1.0
HG X:HG631 3.5 60.4 0.3
CG X:PHE333 3.5 39.8 1.0
CD2 X:PHE333 3.5 40.6 1.0
CA X:CYS361 3.6 46.1 1.0
CD1 X:PHE333 3.6 43.6 1.0
CE2 X:PHE333 3.7 41.5 1.0
C X:ALA357 3.7 40.8 1.0
CE1 X:PHE333 3.8 43.8 1.0
CZ X:PHE333 3.9 44.3 1.0
CA X:ALA357 4.0 40.2 1.0
CB X:ALA357 4.0 40.9 1.0
CB X:ALA360 4.1 48.3 1.0
C X:ALA360 4.1 49.8 1.0
CB X:PHE333 4.2 43.0 1.0
CA X:ALA360 4.6 46.4 1.0
O X:ALA360 4.8 51.6 1.0
N X:ASN358 4.9 40.9 1.0

Mercury binding site 2 out of 6 in 2epm

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Mercury binding site 2 out of 6 in the N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg631

b:60.4
occ:0.30
 SG X:CYS361 2.2 42.6 1.0
CB X:CYS361 2.7 44.5 1.0
CH2 X:TRP393 2.9 40.0 1.0
CZ3 X:TRP393 3.3 39.8 1.0
O X:ALA357 3.3 38.8 1.0
CD1 X:PHE333 3.4 43.6 1.0
HG X:HG630 3.5 48.5 0.7
OH X:TYR84 3.6 37.6 1.0
CG2 X:VAL369 3.6 40.1 1.0
C X:ALA357 3.6 40.8 1.0
CA X:ASN358 3.8 42.4 1.0
CE1 X:PHE333 3.8 43.8 1.0
N X:ASN358 3.8 40.9 1.0
CZ X:TYR84 4.1 40.5 1.0
CZ2 X:TRP393 4.1 45.2 1.0
CA X:CYS361 4.1 46.1 1.0
CG X:PHE333 4.1 39.8 1.0
CB X:ALA357 4.4 40.9 1.0
N X:CYS361 4.4 48.1 1.0
CB X:PHE333 4.5 43.0 1.0
CE2 X:TYR84 4.6 35.5 1.0
CG1 X:VAL369 4.6 43.2 1.0
CA X:ALA357 4.6 40.2 1.0
CE3 X:TRP393 4.6 42.5 1.0
C X:ASN358 4.7 40.9 1.0
CE1 X:TYR84 4.7 38.5 1.0
O X:ASN358 4.7 45.2 1.0
CB X:VAL369 4.8 38.2 1.0
CB X:ASN358 4.8 39.6 1.0
CZ X:PHE333 4.9 44.3 1.0

Mercury binding site 3 out of 6 in 2epm

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Mercury binding site 3 out of 6 in the N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg632

b:44.5
occ:0.90
 SG X:CYS164 2.3 36.3 1.0
O X:HOH769 2.8 50.9 1.0
ND2 X:ASN219 3.1 43.0 1.0
CB X:CYS164 3.3 34.2 1.0
OE1 X:GLU120 3.3 37.2 1.0
SD X:MET90 3.5 34.8 1.0
CG X:ASN219 3.6 42.8 1.0
CB X:ASN219 3.8 38.6 1.0
CG X:MET90 4.2 34.6 1.0
OD1 X:ASN219 4.4 34.3 1.0
CD X:GLU120 4.5 38.5 1.0
O X:HOH874 4.5 35.0 1.0
CA X:CYS164 4.5 35.4 1.0
CB X:MET90 4.7 34.3 1.0
OE1 X:GLN265 4.7 56.9 1.0
CG2 X:ILE370 4.9 39.7 1.0
CD1 X:ILE370 4.9 43.1 1.0

Mercury binding site 4 out of 6 in 2epm

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Mercury binding site 4 out of 6 in the N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg634

b:61.9
occ:0.50
 SG X:CYS247 2.4 53.4 0.5
CG X:TYR294 3.1 84.2 1.0
CD1 X:TYR294 3.2 82.2 1.0
CB X:CYS247 3.4 48.2 0.5
CB X:CYS247 3.4 48.6 0.5
C X:CYS247 3.4 44.0 1.0
O X:CYS247 3.5 45.1 1.0
CB X:TYR294 3.5 78.6 1.0
CD2 X:TYR294 3.6 88.5 1.0
N X:GLN248 3.7 47.9 1.0
CE1 X:TYR294 3.7 88.1 1.0
CA X:CYS247 4.0 47.7 0.5
CA X:CYS247 4.0 47.5 0.5
CE2 X:TYR294 4.0 88.5 1.0
CZ X:TYR294 4.1 90.7 1.0
CA X:GLN248 4.1 49.1 1.0
OE1 X:GLU251 4.5 65.6 1.0
SG X:CYS247 4.7 51.4 0.5
O X:LEU244 4.8 52.0 1.0
CD1 X:LEU298 4.8 57.4 1.0
CA X:TYR294 4.9 72.2 1.0

Mercury binding site 5 out of 6 in 2epm

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Mercury binding site 5 out of 6 in the N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg635

b:62.7
occ:0.20
 SG X:CYS587 1.9 58.9 1.0
CB X:CYS587 3.1 49.7 1.0
N X:CYS587 3.7 48.9 1.0
OE2 X:GLU589 3.9 71.0 1.0
CA X:CYS587 3.9 46.4 1.0
CD X:GLU589 4.2 61.8 1.0
O X:HOH906 4.2 63.5 1.0
C X:ASP586 4.3 50.7 1.0
CB X:ASP586 4.4 54.9 1.0
O X:CYS587 4.4 40.5 1.0
C X:CYS587 4.4 42.2 1.0
CG X:GLU589 4.5 53.2 1.0
OE1 X:GLU589 4.7 53.8 1.0
CA X:ASP586 4.8 50.8 1.0
O X:ASP586 4.9 48.6 1.0
N X:ASP586 5.0 50.4 1.0

Mercury binding site 6 out of 6 in 2epm

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Mercury binding site 6 out of 6 in the N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of N-Acetyl-B-D-Glucoasminidase (Gcna) From Stretococcus Gordonii within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Hg636

b:47.3
occ:0.20
 CG X:MET270 1.8 57.3 0.5
CE X:MET270 1.9 25.7 0.5
SD X:MET270 2.2 60.3 0.5
CG X:MET270 2.4 46.7 0.5
SD X:MET270 2.8 32.0 0.5
CD2 X:LEU295 2.9 79.6 1.0
CB X:MET270 3.2 54.7 0.5
CB X:MET270 3.3 49.8 0.5
O X:MET270 3.4 58.4 1.0
CE X:MET270 3.6 61.7 0.5
SG X:CYS247 3.7 51.4 0.5
C X:MET270 3.8 53.8 1.0
CB X:MET246 3.9 47.2 1.0
CA X:MET270 3.9 54.7 0.5
CA X:MET270 3.9 50.2 0.5
O X:SER243 4.1 54.6 1.0
CG X:LEU295 4.3 76.1 1.0
N X:CYS247 4.4 49.0 1.0
C X:MET246 4.5 47.8 1.0
CE1 X:PHE271 4.6 57.7 1.0
N X:PHE271 4.6 53.7 1.0
CA X:CYS247 4.8 47.5 0.5
CA X:CYS247 4.8 47.7 0.5
CD1 X:PHE271 4.8 55.6 1.0
CZ X:PHE271 4.8 58.1 1.0
CA X:MET246 4.9 45.7 1.0
CG X:MET246 4.9 50.8 1.0
O X:MET246 4.9 44.6 1.0
CB X:CYS247 4.9 48.2 0.5
CA X:SER243 4.9 51.8 1.0
CB X:CYS247 5.0 48.6 0.5
C X:SER243 5.0 51.4 1.0

Reference:

D.B.Langley, D.W.S.Harty, N.A.Jacques, N.Hunter, J.M.Guss, C.A.Collyer. Structure of N-Acetyl-Beta-D-Glucosaminidase (Gcna) From the Endocarditis Pathogen Streptococcus Gordonii and Its Complex with the Mechanism-Based Inhibitor Nag-Thiazoline J.Mol.Biol. V. 377 104 2008.
ISSN: ISSN 0022-2836
PubMed: 18237743
DOI: 10.1016/J.JMB.2007.09.028
Page generated: Sun Aug 11 02:25:33 2024

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