Atomistry » Mercury » PDB 1yu1-2epm » 2epm
Atomistry »
  Mercury »
    PDB 1yu1-2epm »
      2epm »

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

Go back to Mercury Binding Sites List in 2epm
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

Go back to Mercury Binding Sites List in 2epm
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

Go back to Mercury Binding Sites List in 2epm
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

Go back to Mercury Binding Sites List in 2epm
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

Go back to Mercury Binding Sites List in 2epm
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

Go back to Mercury Binding Sites List in 2epm
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy