Zinc in PDB 2ynw: Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases
Protein crystallography data
The structure of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases, PDB code: 2ynw
was solved by
P.S.Borra,
O.Samuelsen,
J.Spencer,
M.S.Lorentzen,
H.-K.S.Leiros,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.861 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.160,
135.534,
38.541,
90.00,
90.83,
90.00
|
R / Rfree (%)
|
16.69 /
19.86
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases
(pdb code 2ynw). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases, PDB code: 2ynw:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2ynw
Go back to
Zinc Binding Sites List in 2ynw
Zinc binding site 1 out
of 4 in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1296
b:6.8
occ:1.00
|
O
|
A:HOH2053
|
2.0
|
9.0
|
1.0
|
ND1
|
A:HIS118
|
2.0
|
7.2
|
1.0
|
NE2
|
A:HIS196
|
2.1
|
6.2
|
1.0
|
NE2
|
A:HIS116
|
2.1
|
3.6
|
1.0
|
CE1
|
A:HIS118
|
2.9
|
10.0
|
1.0
|
CD2
|
A:HIS196
|
3.0
|
6.5
|
1.0
|
CE1
|
A:HIS116
|
3.0
|
3.7
|
1.0
|
HB2
|
A:HIS118
|
3.0
|
7.1
|
1.0
|
CG
|
A:HIS118
|
3.1
|
7.2
|
1.0
|
HE1
|
A:HIS118
|
3.1
|
12.0
|
1.0
|
CD2
|
A:HIS116
|
3.1
|
2.9
|
1.0
|
HD2
|
A:HIS196
|
3.1
|
7.8
|
1.0
|
CE1
|
A:HIS196
|
3.1
|
15.7
|
1.0
|
HE1
|
A:HIS116
|
3.2
|
4.4
|
1.0
|
HD2
|
A:HIS116
|
3.3
|
3.4
|
1.0
|
HE1
|
A:HIS196
|
3.3
|
18.8
|
1.0
|
CB
|
A:HIS118
|
3.5
|
5.9
|
1.0
|
ZN
|
A:ZN1297
|
3.5
|
9.8
|
1.0
|
HB2
|
A:CYS221
|
3.6
|
8.1
|
1.0
|
HB3
|
A:HIS118
|
3.7
|
7.1
|
1.0
|
O
|
B:HOH2011
|
3.8
|
17.6
|
1.0
|
HG21
|
A:THR197
|
3.9
|
12.6
|
1.0
|
OD1
|
A:ASP120
|
4.0
|
8.0
|
1.0
|
HB3
|
A:CYS221
|
4.0
|
8.1
|
1.0
|
HG22
|
A:THR197
|
4.0
|
12.6
|
1.0
|
NE2
|
A:HIS118
|
4.1
|
13.1
|
1.0
|
CB
|
A:CYS221
|
4.1
|
6.8
|
1.0
|
ND1
|
A:HIS116
|
4.1
|
1.9
|
1.0
|
CD2
|
A:HIS118
|
4.1
|
10.6
|
1.0
|
CG
|
A:HIS196
|
4.2
|
5.7
|
1.0
|
ND1
|
A:HIS196
|
4.2
|
6.8
|
1.0
|
CG
|
A:HIS116
|
4.2
|
0.4
|
1.0
|
SG
|
A:CYS221
|
4.2
|
6.7
|
1.0
|
CG2
|
A:THR197
|
4.4
|
10.5
|
1.0
|
OD2
|
A:ASP120
|
4.5
|
4.7
|
1.0
|
HG2
|
A:ARG121
|
4.6
|
3.6
|
1.0
|
H
|
A:HIS118
|
4.6
|
2.7
|
1.0
|
CG
|
A:ASP120
|
4.7
|
10.6
|
1.0
|
O2
|
B:SO41298
|
4.7
|
37.7
|
1.0
|
HG23
|
A:THR197
|
4.8
|
12.6
|
1.0
|
HE2
|
A:HIS118
|
4.8
|
15.7
|
1.0
|
CA
|
A:HIS118
|
4.9
|
6.1
|
1.0
|
HD1
|
A:HIS116
|
4.9
|
2.3
|
1.0
|
HA2
|
B:GLY63
|
5.0
|
21.7
|
1.0
|
HG3
|
A:ARG121
|
5.0
|
3.6
|
1.0
|
HD1
|
A:HIS196
|
5.0
|
8.2
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2ynw
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Zinc Binding Sites List in 2ynw
Zinc binding site 2 out
of 4 in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1297
b:9.8
occ:1.00
|
O
|
A:HOH2053
|
2.0
|
9.0
|
1.0
|
OD2
|
A:ASP120
|
2.0
|
4.7
|
1.0
|
NE2
|
A:HIS263
|
2.1
|
6.5
|
1.0
|
SG
|
A:CYS221
|
2.3
|
6.7
|
1.0
|
CG
|
A:ASP120
|
3.0
|
10.6
|
1.0
|
CD2
|
A:HIS263
|
3.1
|
7.1
|
1.0
|
CE1
|
A:HIS263
|
3.1
|
8.8
|
1.0
|
HD2
|
A:HIS263
|
3.2
|
8.5
|
1.0
|
HE1
|
A:HIS263
|
3.3
|
10.5
|
1.0
|
HB3
|
A:CYS221
|
3.3
|
8.1
|
1.0
|
HH21
|
A:ARG121
|
3.3
|
6.0
|
1.0
|
HE
|
A:ARG121
|
3.4
|
5.9
|
1.0
|
OD1
|
A:ASP120
|
3.4
|
8.0
|
1.0
|
CB
|
A:CYS221
|
3.4
|
6.8
|
1.0
|
ZN
|
A:ZN1296
|
3.5
|
6.8
|
1.0
|
HE1
|
A:HIS116
|
3.5
|
4.4
|
1.0
|
O
|
B:HOH2011
|
3.7
|
17.6
|
1.0
|
O
|
B:GLY63
|
3.7
|
16.5
|
1.0
|
HB2
|
A:CYS221
|
3.7
|
8.1
|
1.0
|
NH2
|
A:ARG121
|
3.9
|
5.0
|
1.0
|
NE
|
A:ARG121
|
3.9
|
4.9
|
1.0
|
ND1
|
A:HIS263
|
4.2
|
5.8
|
1.0
|
CE1
|
A:HIS116
|
4.2
|
3.7
|
1.0
|
CG
|
A:HIS263
|
4.2
|
4.3
|
1.0
|
CZ
|
A:ARG121
|
4.3
|
4.5
|
1.0
|
CB
|
A:ASP120
|
4.3
|
6.3
|
1.0
|
NE2
|
A:HIS196
|
4.3
|
6.2
|
1.0
|
NE2
|
A:HIS116
|
4.3
|
3.6
|
1.0
|
HA3
|
A:GLY262
|
4.3
|
4.3
|
1.0
|
HB2
|
A:ASP120
|
4.4
|
7.5
|
1.0
|
HH22
|
A:ARG121
|
4.5
|
6.0
|
1.0
|
HG2
|
A:ARG121
|
4.5
|
3.6
|
1.0
|
HB3
|
A:ASP120
|
4.6
|
7.5
|
1.0
|
HE1
|
A:HIS196
|
4.6
|
18.8
|
1.0
|
O
|
A:HOH2104
|
4.6
|
13.8
|
1.0
|
HA
|
B:TYR64
|
4.7
|
12.9
|
1.0
|
CA
|
A:CYS221
|
4.7
|
4.7
|
1.0
|
CE1
|
A:HIS196
|
4.7
|
15.7
|
1.0
|
HA
|
A:CYS221
|
4.7
|
5.7
|
1.0
|
C
|
B:GLY63
|
4.7
|
17.4
|
1.0
|
HD2
|
A:ARG121
|
4.8
|
4.6
|
1.0
|
HB2
|
A:HIS118
|
4.9
|
7.1
|
1.0
|
CD
|
A:ARG121
|
4.9
|
3.8
|
1.0
|
HD1
|
A:HIS263
|
4.9
|
7.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2ynw
Go back to
Zinc Binding Sites List in 2ynw
Zinc binding site 3 out
of 4 in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1296
b:10.8
occ:1.00
|
ND1
|
B:HIS118
|
1.9
|
9.4
|
1.0
|
NE2
|
B:HIS196
|
2.0
|
6.5
|
1.0
|
O
|
A:HOH2017
|
2.1
|
10.2
|
1.0
|
NE2
|
B:HIS116
|
2.1
|
8.2
|
1.0
|
CE1
|
B:HIS118
|
2.9
|
9.8
|
1.0
|
HB2
|
B:HIS118
|
2.9
|
12.9
|
1.0
|
CG
|
B:HIS118
|
3.0
|
11.2
|
1.0
|
CE1
|
B:HIS116
|
3.0
|
10.5
|
1.0
|
CD2
|
B:HIS196
|
3.0
|
8.1
|
1.0
|
CE1
|
B:HIS196
|
3.0
|
16.1
|
1.0
|
CD2
|
B:HIS116
|
3.1
|
10.7
|
1.0
|
HE1
|
B:HIS118
|
3.1
|
11.8
|
1.0
|
HE1
|
B:HIS116
|
3.2
|
12.6
|
1.0
|
HD2
|
B:HIS196
|
3.2
|
9.7
|
1.0
|
HE1
|
B:HIS196
|
3.2
|
19.4
|
1.0
|
HD2
|
B:HIS116
|
3.3
|
12.9
|
1.0
|
CB
|
B:HIS118
|
3.3
|
10.7
|
1.0
|
ZN
|
B:ZN1297
|
3.5
|
13.3
|
1.0
|
HB3
|
B:HIS118
|
3.5
|
12.9
|
1.0
|
HB2
|
B:CYS221
|
3.7
|
10.9
|
1.0
|
O
|
A:HOH2019
|
3.9
|
17.0
|
1.0
|
OD1
|
B:ASP120
|
3.9
|
9.9
|
1.0
|
HG21
|
B:THR197
|
3.9
|
16.8
|
1.0
|
HB3
|
B:CYS221
|
4.0
|
10.9
|
1.0
|
NE2
|
B:HIS118
|
4.0
|
16.2
|
1.0
|
CD2
|
B:HIS118
|
4.1
|
12.1
|
1.0
|
ND1
|
B:HIS116
|
4.1
|
8.1
|
1.0
|
HG22
|
B:THR197
|
4.1
|
16.8
|
1.0
|
CB
|
B:CYS221
|
4.1
|
9.1
|
1.0
|
ND1
|
B:HIS196
|
4.1
|
9.6
|
1.0
|
CG
|
B:HIS196
|
4.2
|
12.2
|
1.0
|
CG
|
B:HIS116
|
4.2
|
5.9
|
1.0
|
SG
|
B:CYS221
|
4.2
|
11.2
|
1.0
|
CG2
|
B:THR197
|
4.5
|
14.0
|
1.0
|
HG2
|
B:ARG121
|
4.5
|
12.1
|
1.0
|
OD2
|
B:ASP120
|
4.5
|
9.4
|
1.0
|
H
|
B:HIS118
|
4.6
|
8.8
|
1.0
|
CG
|
B:ASP120
|
4.7
|
8.2
|
1.0
|
HE2
|
B:HIS118
|
4.8
|
19.5
|
1.0
|
CA
|
B:HIS118
|
4.8
|
8.7
|
1.0
|
HG3
|
B:ARG121
|
4.8
|
12.1
|
1.0
|
HG23
|
B:THR197
|
4.8
|
16.8
|
1.0
|
HD1
|
B:HIS116
|
4.9
|
9.7
|
1.0
|
HD2
|
B:HIS118
|
4.9
|
14.6
|
1.0
|
HD1
|
B:HIS196
|
4.9
|
11.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2ynw
Go back to
Zinc Binding Sites List in 2ynw
Zinc binding site 4 out
of 4 in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1297
b:13.3
occ:1.00
|
O
|
A:HOH2017
|
2.0
|
10.2
|
1.0
|
OD2
|
B:ASP120
|
2.0
|
9.4
|
1.0
|
NE2
|
B:HIS263
|
2.2
|
7.3
|
1.0
|
SG
|
B:CYS221
|
2.3
|
11.2
|
1.0
|
CG
|
B:ASP120
|
3.0
|
8.2
|
1.0
|
CD2
|
B:HIS263
|
3.1
|
15.0
|
1.0
|
CE1
|
B:HIS263
|
3.1
|
13.5
|
1.0
|
HD2
|
B:HIS263
|
3.3
|
18.0
|
1.0
|
HE1
|
B:HIS263
|
3.3
|
16.2
|
1.0
|
OD1
|
B:ASP120
|
3.3
|
9.9
|
1.0
|
HB3
|
B:CYS221
|
3.3
|
10.9
|
1.0
|
HE
|
B:ARG121
|
3.3
|
9.7
|
1.0
|
HH21
|
B:ARG121
|
3.4
|
13.2
|
1.0
|
CB
|
B:CYS221
|
3.4
|
9.1
|
1.0
|
ZN
|
B:ZN1296
|
3.5
|
10.8
|
1.0
|
HE1
|
B:HIS116
|
3.6
|
12.6
|
1.0
|
O
|
A:GLY63
|
3.7
|
14.8
|
1.0
|
HB2
|
B:CYS221
|
3.8
|
10.9
|
1.0
|
O
|
A:HOH2019
|
3.8
|
17.0
|
1.0
|
NE
|
B:ARG121
|
3.9
|
8.1
|
1.0
|
NH2
|
B:ARG121
|
3.9
|
11.0
|
1.0
|
ND1
|
B:HIS263
|
4.2
|
9.5
|
1.0
|
CG
|
B:HIS263
|
4.2
|
10.7
|
1.0
|
CZ
|
B:ARG121
|
4.2
|
11.4
|
1.0
|
CE1
|
B:HIS116
|
4.2
|
10.5
|
1.0
|
CB
|
B:ASP120
|
4.3
|
8.7
|
1.0
|
NE2
|
B:HIS116
|
4.3
|
8.2
|
1.0
|
HA3
|
B:GLY262
|
4.3
|
8.3
|
1.0
|
HB2
|
B:ASP120
|
4.3
|
10.4
|
1.0
|
NE2
|
B:HIS196
|
4.4
|
6.5
|
1.0
|
HG2
|
B:ARG121
|
4.4
|
12.1
|
1.0
|
HH22
|
B:ARG121
|
4.5
|
13.2
|
1.0
|
HB3
|
B:ASP120
|
4.6
|
10.4
|
1.0
|
HA
|
A:TYR64
|
4.6
|
13.9
|
1.0
|
HE1
|
B:HIS196
|
4.6
|
19.4
|
1.0
|
C
|
A:GLY63
|
4.7
|
13.9
|
1.0
|
HD2
|
B:ARG121
|
4.7
|
14.1
|
1.0
|
CA
|
B:CYS221
|
4.7
|
10.6
|
1.0
|
HA
|
B:CYS221
|
4.8
|
12.7
|
1.0
|
O
|
B:HOH2057
|
4.8
|
16.9
|
1.0
|
CE1
|
B:HIS196
|
4.8
|
16.1
|
1.0
|
CD
|
B:ARG121
|
4.8
|
11.8
|
1.0
|
HB2
|
B:HIS118
|
4.8
|
12.9
|
1.0
|
HD1
|
B:HIS263
|
5.0
|
11.4
|
1.0
|
HG
|
B:SER69
|
5.0
|
17.4
|
1.0
|
O
|
B:GLY262
|
5.0
|
9.3
|
1.0
|
|
Reference:
P.S.Borra,
O.Samuelsen,
J.Spencer,
T.R.Walsh,
M.S.Lorentzen,
H.-K.S.Leiros.
Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active- Site Plasticity in Metallo-Beta-Lactamases. Antimicrob.Agents Chemother. V. 57 848 2013.
ISSN: ISSN 0066-4804
PubMed: 23208706
DOI: 10.1128/AAC.02227-12
Page generated: Thu Oct 17 05:53:51 2024
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