Atomistry » Zinc » PDB 5n34-5nek » 5nde
Atomistry »
  Zinc »
    PDB 5n34-5nek »
      5nde »

Zinc in PDB 5nde: Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222

Enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222, PDB code: 5nde was solved by P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.26 / 1.70
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 130.740, 130.740, 100.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 17.3

Other elements in 5nde:

The structure of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 (pdb code 5nde). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222, PDB code: 5nde:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 1 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:20.3
occ:0.94
 OD1 A:ASP37 1.9 27.9 1.0
NE2 A:HIS35 2.1 25.1 1.0
CG A:ASP37 2.9 45.4 1.0
CE1 A:HIS35 3.0 39.9 1.0
O A:HOH501 3.0 39.5 1.0
CD2 A:HIS35 3.1 24.3 1.0
OD2 A:ASP37 3.3 34.6 1.0
O A:HOH654 4.0 41.3 1.0
ND1 A:HIS35 4.2 33.7 1.0
CG A:HIS35 4.2 25.2 1.0
CB A:ASP37 4.3 42.6 1.0
CA A:ASP37 4.9 31.6 1.0
CG2 A:THR43 5.0 27.5 1.0

Zinc binding site 2 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 2 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:21.7
occ:1.00
 ND1 A:HIS110 2.0 21.1 1.0
NE2 A:HIS197 2.1 22.2 1.0
NE2 A:HIS108 2.1 19.5 1.0
CE1 A:HIS110 2.9 21.1 1.0
CD2 A:HIS108 3.0 20.6 1.0
CG A:HIS110 3.0 20.6 1.0
CD2 A:HIS197 3.1 20.4 1.0
CE1 A:HIS197 3.1 24.7 1.0
CE1 A:HIS108 3.2 20.6 1.0
ZN A:ZN403 3.4 23.7 0.8
CB A:HIS110 3.4 20.1 1.0
O1 A:GOL411 3.6 40.5 1.0
OD1 A:ASP112 4.0 23.2 1.0
O A:HOH511 4.0 35.3 1.0
NE2 A:HIS110 4.1 24.2 1.0
SG A:CYS222 4.1 23.4 1.0
CD2 A:HIS110 4.1 23.6 1.0
CB A:CYS222 4.1 23.2 1.0
CG A:HIS108 4.2 19.8 1.0
ND1 A:HIS197 4.2 21.6 1.0
CG A:HIS197 4.2 18.6 1.0
ND1 A:HIS108 4.2 22.6 1.0
OD2 A:ASP112 4.4 30.8 1.0
C1 A:GOL411 4.5 28.8 1.0
C3 A:GOL410 4.6 80.6 1.0
CG A:ASP112 4.6 26.1 1.0
O2 A:GOL411 4.6 67.0 1.0
O2 A:GOL410 4.7 75.9 1.0
O3 A:GOL410 4.9 83.5 1.0
CA A:HIS110 4.9 18.8 1.0

Zinc binding site 3 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 3 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:23.7
occ:0.82
 O1 A:GOL411 2.0 40.5 1.0
NE2 A:HIS264 2.0 25.8 1.0
OD2 A:ASP112 2.1 30.8 1.0
SG A:CYS222 2.2 23.4 1.0
CD2 A:HIS264 3.0 27.1 1.0
CE1 A:HIS264 3.0 26.8 1.0
CG A:ASP112 3.1 26.1 1.0
OD1 A:ASP112 3.3 23.2 1.0
C1 A:GOL411 3.4 28.8 1.0
CB A:CYS222 3.4 23.2 1.0
ZN A:ZN402 3.4 21.7 1.0
O A:HOH511 3.5 35.3 1.0
ND1 A:HIS264 4.1 23.0 1.0
CG A:HIS264 4.1 24.9 1.0
C2 A:GOL411 4.1 49.1 1.0
CE1 A:HIS108 4.2 20.6 1.0
NE2 A:HIS108 4.2 19.5 1.0
NE2 A:HIS197 4.3 22.2 1.0
O2 A:GOL411 4.4 67.0 1.0
CB A:ASP112 4.4 18.6 1.0
CA A:CYS222 4.6 20.0 1.0
CE1 A:HIS197 4.7 24.7 1.0
O A:HOH577 4.8 24.0 1.0
O A:GLY263 4.9 22.6 1.0
O A:ASP112 4.9 22.2 1.0
CA A:GLY263 4.9 20.2 1.0
C A:GLY263 4.9 21.0 1.0
O A:HOH629 5.0 25.1 1.0

Zinc binding site 4 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 4 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:25.1
occ:1.00
 ND1 A:HIS165 2.0 26.0 1.0
OE2 A:GLU118 2.1 24.7 1.0
CD A:GLU118 2.9 31.7 1.0
CE1 A:HIS165 2.9 26.7 1.0
CG A:HIS165 3.0 28.1 1.0
OE1 A:GLU118 3.1 31.6 1.0
CB A:HIS165 3.4 27.2 1.0
O A:HOH556 3.8 29.6 1.0
NE2 A:HIS165 4.0 29.1 1.0
O A:HIS165 4.0 31.1 1.0
CD2 A:HIS165 4.1 27.9 1.0
N A:HIS165 4.1 28.2 1.0
CG A:GLU118 4.2 27.5 1.0
CA A:HIS165 4.3 25.4 1.0
C A:HIS165 4.6 27.1 1.0
ND2 A:ASN83 4.9 27.0 1.0

Zinc binding site 5 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 5 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:22.0
occ:1.00
 ND1 B:HIS110 2.1 20.8 1.0
NE2 B:HIS197 2.1 21.8 1.0
NE2 B:HIS108 2.1 18.5 1.0
O B:HOH638 2.2 27.1 1.0
CD2 B:HIS108 3.0 18.2 1.0
CD2 B:HIS197 3.0 20.3 1.0
CE1 B:HIS110 3.0 23.3 1.0
CG B:HIS110 3.1 19.7 1.0
CE1 B:HIS197 3.1 24.3 1.0
CE1 B:HIS108 3.2 19.9 1.0
CB B:HIS110 3.4 16.9 1.0
ZN B:ZN402 3.5 27.3 0.9
O B:HOH507 3.8 38.9 1.0
OD1 B:ASP112 3.9 22.4 1.0
SG B:CYS222 4.1 26.7 1.0
NE2 B:HIS110 4.1 24.1 1.0
CB B:CYS222 4.2 23.1 1.0
CD2 B:HIS110 4.2 21.4 1.0
CG B:HIS197 4.2 19.4 1.0
ND1 B:HIS197 4.2 20.6 1.0
CG B:HIS108 4.2 17.2 1.0
O1 B:GOL404 4.2 30.9 1.0
ND1 B:HIS108 4.2 19.9 1.0
OD2 B:ASP112 4.4 25.9 1.0
CG B:ASP112 4.6 23.9 1.0
C1 B:GOL404 4.9 42.7 1.0
CA B:HIS110 4.9 17.2 1.0

Zinc binding site 6 out of 6 in 5nde

Go back to Zinc Binding Sites List in 5nde
Zinc binding site 6 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Metallo-Beta-Lactamase Spm-1 in Space Group P4222 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:27.3
occ:0.86
 O B:HOH638 1.9 27.1 1.0
OD2 B:ASP112 2.1 25.9 1.0
NE2 B:HIS264 2.1 23.1 1.0
SG B:CYS222 2.2 26.7 1.0
O1 B:GOL404 2.9 30.9 1.0
CD2 B:HIS264 3.0 28.7 1.0
CE1 B:HIS264 3.1 26.8 1.0
CG B:ASP112 3.1 23.9 1.0
O B:HOH507 3.3 38.9 1.0
CB B:CYS222 3.4 23.1 1.0
OD1 B:ASP112 3.4 22.4 1.0
ZN B:ZN401 3.5 22.0 1.0
O B:HOH501 3.5 40.1 1.0
O B:HOH561 4.1 59.2 1.0
C1 B:GOL404 4.2 42.7 1.0
ND1 B:HIS264 4.2 24.5 1.0
CG B:HIS264 4.2 25.1 1.0
O2 B:GOL404 4.2 70.5 1.0
CE1 B:HIS108 4.2 19.9 1.0
NE2 B:HIS108 4.2 18.5 1.0
NE2 B:HIS197 4.3 21.8 1.0
CB B:ASP112 4.4 16.9 1.0
CA B:CYS222 4.6 25.6 1.0
CE1 B:HIS197 4.7 24.3 1.0
C2 B:GOL404 4.8 66.1 1.0
O B:GLY263 4.9 23.0 1.0
CA B:GLY263 5.0 20.3 1.0
O B:ASP112 5.0 19.4 1.0
O B:HOH652 5.0 28.9 1.0
C B:GLY263 5.0 25.1 1.0

Reference:

M.I.Abboud, M.Kosmopoulou, A.P.Krismanich, J.W.Johnson, P.Hinchliffe, J.Brem, T.D.W.Claridge, J.Spencer, C.J.Schofield, G.I.Dmitrienko. Cyclobutanone Mimics of Intermediates in Metallo-Beta-Lactamase Catalysis. Chemistry V. 24 5734 2018.
ISSN: ISSN 1521-3765
PubMed: 29250863
DOI: 10.1002/CHEM.201705886
Page generated: Sun Oct 27 22:45:30 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy