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Zinc in PDB 5mmd: Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding

Protein crystallography data

The structure of Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding, PDB code: 5mmd was solved by S.Skagseth, T.Christopeit, S.Akhter, A.Bayer, O.Samuelsen, H.-K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.29 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.398, 127.195, 44.274, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.8

Other elements in 5mmd:

The structure of Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding (pdb code 5mmd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding, PDB code: 5mmd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5mmd

Go back to Zinc Binding Sites List in 5mmd
Zinc binding site 1 out of 6 in the Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:15.8
occ:0.95
OD2 E:ASP120 2.0 8.8 1.0
O E:HOH649 2.1 15.1 1.0
NE2 E:HIS263 2.2 11.8 1.0
SG E:CYS221 2.4 16.2 1.0
CG E:ASP120 3.0 11.7 1.0
CD2 E:HIS263 3.0 12.2 1.0
HE2 E:LYS121 3.1 10.7 1.0
HD2 E:HIS263 3.2 14.6 1.0
CE1 E:HIS263 3.2 13.8 1.0
HB3 E:CYS221 3.4 14.8 1.0
OD1 E:ASP120 3.4 13.1 1.0
HE1 E:HIS263 3.4 16.6 1.0
ZN E:ZN403 3.5 14.4 1.0
CB E:CYS221 3.5 12.3 1.0
HE1 E:HIS116 3.5 14.7 1.0
O E:HOH717 3.7 26.7 1.0
HB2 E:CYS221 3.8 14.8 1.0
O E:HOH696 3.9 30.3 1.0
CE E:LYS121 4.1 8.9 1.0
CE1 E:HIS116 4.2 12.3 1.0
CG E:HIS263 4.2 12.2 1.0
ND1 E:HIS263 4.3 13.4 1.0
NE2 E:HIS196 4.3 11.4 1.0
NE2 E:HIS116 4.3 13.8 1.0
HE3 E:LYS121 4.3 10.7 1.0
HG2 E:LYS121 4.3 10.9 1.0
CB E:ASP120 4.4 9.0 1.0
HZ1 E:LYS121 4.4 11.9 1.0
HE1 E:HIS196 4.4 16.3 1.0
HB2 E:ASP120 4.5 10.8 1.0
CE1 E:HIS196 4.5 13.6 1.0
HB3 E:ASP120 4.6 10.8 1.0
NZ E:LYS121 4.6 9.9 1.0
HZ3 E:LYS121 4.7 11.9 1.0
HA3 E:GLY262 4.7 12.3 1.0
HB2 E:HIS118 4.7 14.1 1.0
CA E:CYS221 4.8 11.7 1.0
HA E:CYS221 4.8 14.0 1.0
O E:HOH655 4.9 15.6 1.0
O E:HOH610 5.0 14.3 1.0

Zinc binding site 2 out of 6 in 5mmd

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Zinc binding site 2 out of 6 in the Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:36.2
occ:1.00
ND1 E:HIS285 2.1 19.2 1.0
O E:HOH724 2.5 34.7 1.0
O E:HOH560 2.6 51.1 1.0
O E:HOH702 2.7 43.9 1.0
CE1 E:HIS285 2.9 18.2 1.0
O E:HOH728 3.1 42.9 1.0
HE1 E:HIS285 3.1 21.9 1.0
CG E:HIS285 3.1 17.1 1.0
HA E:HIS285 3.1 21.3 1.0
HB2 E:HIS285 3.3 21.1 1.0
CB E:HIS285 3.5 17.6 1.0
CA E:HIS285 3.8 17.8 1.0
HD22 E:LEU226 3.9 25.3 0.6
NE2 E:HIS285 4.1 16.1 1.0
CD2 E:HIS285 4.2 15.4 1.0
HD23 E:LEU226 4.2 25.3 0.6
CD2 E:LEU226 4.4 21.1 0.6
HB3 E:HIS285 4.5 21.1 1.0
HB E:VAL288 4.6 23.4 1.0
HD21 E:LEU226 4.6 25.3 0.6
O E:HIS285 4.7 16.7 1.0
C E:HIS285 4.7 16.4 1.0
HD21 E:LEU289 4.7 22.7 1.0
HG11 E:VAL288 4.8 25.1 1.0
N E:HIS285 4.9 17.3 1.0
HG E:LEU289 4.9 19.9 1.0

Zinc binding site 3 out of 6 in 5mmd

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Zinc binding site 3 out of 6 in the Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn403

b:14.4
occ:1.00
O E:HOH649 1.8 15.1 1.0
NE2 E:HIS196 1.9 11.4 1.0
ND1 E:HIS118 2.0 12.8 1.0
NE2 E:HIS116 2.1 13.8 1.0
HB2 E:HIS118 2.9 14.1 1.0
CE1 E:HIS196 2.9 13.6 1.0
CD2 E:HIS196 3.0 11.9 1.0
CG E:HIS118 3.0 12.6 1.0
CE1 E:HIS118 3.0 13.7 1.0
HE1 E:HIS196 3.1 16.3 1.0
CD2 E:HIS116 3.1 14.2 1.0
CE1 E:HIS116 3.1 12.3 1.0
HD2 E:HIS196 3.2 14.3 1.0
HE1 E:HIS118 3.2 16.4 1.0
HD2 E:HIS116 3.3 17.0 1.0
HE1 E:HIS116 3.3 14.7 1.0
CB E:HIS118 3.3 11.7 1.0
ZN E:ZN401 3.5 15.8 0.9
HB3 E:HIS118 3.5 14.1 1.0
HB2 E:CYS221 3.7 14.8 1.0
ND1 E:HIS196 4.0 13.3 1.0
HG23 E:THR197 4.0 16.6 1.0
OD1 E:ASP120 4.0 13.1 1.0
CG E:HIS196 4.1 12.3 1.0
O E:HOH717 4.1 26.7 1.0
NE2 E:HIS118 4.1 14.3 1.0
HG21 E:THR197 4.1 16.6 1.0
CD2 E:HIS118 4.1 14.1 1.0
HB3 E:CYS221 4.2 14.8 1.0
ND1 E:HIS116 4.2 11.4 1.0
CB E:CYS221 4.2 12.3 1.0
CG E:HIS116 4.3 13.2 1.0
SG E:CYS221 4.3 16.2 1.0
HD2 E:TYR233 4.5 20.7 1.0
H E:HIS118 4.5 14.6 1.0
CG2 E:THR197 4.6 13.8 1.0
OD2 E:ASP120 4.6 8.8 1.0
CA E:HIS118 4.7 12.9 1.0
CG E:ASP120 4.7 11.7 1.0
HD2 E:HIS118 5.0 16.9 1.0

Zinc binding site 4 out of 6 in 5mmd

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Zinc binding site 4 out of 6 in the Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:43.7
occ:1.00
O F:HOH510 1.7 31.4 1.0
NE2 F:HIS263 1.9 28.9 1.0
OD2 F:ASP120 2.3 30.6 1.0
SG F:CYS221 2.4 30.9 1.0
CD2 F:HIS263 2.9 29.3 1.0
CE1 F:HIS263 2.9 28.4 1.0
HD2 F:HIS263 3.1 35.2 1.0
ZN F:ZN402 3.1 18.4 0.7
HE1 F:HIS263 3.1 34.0 1.0
HB3 F:CYS221 3.2 34.7 1.0
HE1 F:HIS116 3.4 37.0 0.6
CB F:CYS221 3.4 28.9 1.0
HE2 F:LYS121 3.4 28.3 1.0
CG F:ASP120 3.4 29.4 1.0
HB2 F:CYS221 3.8 34.7 1.0
HE1 F:HIS116 3.8 34.0 0.4
O F:HOH595 3.9 44.8 1.0
NE2 F:HIS196 3.9 36.1 1.0
OD1 F:ASP120 4.0 30.3 1.0
HE1 F:HIS196 4.0 44.4 1.0
ND1 F:HIS263 4.0 27.9 1.0
CG F:HIS263 4.0 28.8 1.0
NE2 F:HIS116 4.1 29.8 0.4
CE1 F:HIS196 4.1 37.0 1.0
CE1 F:HIS116 4.1 30.8 0.6
CE1 F:HIS116 4.3 28.3 0.4
CE F:LYS121 4.4 23.6 1.0
ZN F:ZN402 4.4 15.6 0.3
HZ1 F:LYS121 4.4 27.8 1.0
NE2 F:HIS116 4.4 40.8 0.6
CB F:ASP120 4.6 26.5 1.0
HA F:CYS221 4.6 33.6 1.0
HB2 F:ASP120 4.6 31.8 1.0
CA F:CYS221 4.7 28.0 1.0
HE3 F:LYS121 4.7 28.3 1.0
HG2 F:LYS121 4.7 29.2 1.0
HZ3 F:LYS121 4.7 27.8 1.0
NZ F:LYS121 4.7 23.1 1.0
CD2 F:HIS196 4.8 36.4 1.0
HB2 F:HIS118 4.8 42.5 1.0
HB3 F:ASP120 4.8 31.8 1.0
HA3 F:GLY262 4.8 29.3 1.0
O F:HOH684 4.9 36.3 1.0

Zinc binding site 5 out of 6 in 5mmd

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Zinc binding site 5 out of 6 in the Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:18.4
occ:0.70
ZN F:ZN402 0.0 18.4 0.7
ZN F:ZN402 1.5 15.6 0.3
O F:HOH510 1.9 31.4 1.0
NE2 F:HIS196 1.9 36.1 1.0
ND1 F:HIS118 2.2 39.8 1.0
NE2 F:HIS116 2.4 40.8 0.6
NE2 F:HIS116 2.6 29.8 0.4
O F:HOH595 2.8 44.8 1.0
CE1 F:HIS196 2.9 37.0 1.0
CD2 F:HIS196 3.0 36.4 1.0
HE1 F:HIS116 3.0 37.0 0.6
HB2 F:HIS118 3.0 42.5 1.0
CE1 F:HIS116 3.0 30.8 0.6
HE1 F:HIS196 3.1 44.4 1.0
ZN F:ZN401 3.1 43.7 1.0
CG F:HIS118 3.1 38.8 1.0
CE1 F:HIS118 3.2 42.6 1.0
HD2 F:HIS196 3.2 43.6 1.0
HE1 F:HIS118 3.3 51.2 1.0
CD2 F:HIS116 3.4 33.0 0.4
HD2 F:HIS116 3.4 39.6 0.4
CB F:HIS118 3.4 35.4 1.0
CD2 F:HIS116 3.5 33.7 0.6
HB3 F:HIS118 3.5 42.5 1.0
CE1 F:HIS116 3.7 28.3 0.4
HD2 F:HIS116 3.8 40.4 0.6
HB2 F:CYS221 3.9 34.7 1.0
HE1 F:HIS116 3.9 34.0 0.4
ND1 F:HIS196 4.0 37.5 1.0
HB3 F:CYS221 4.0 34.7 1.0
CG F:HIS196 4.1 36.9 1.0
OD2 F:ASP120 4.1 30.6 1.0
OD1 F:ASP120 4.1 30.3 1.0
HG23 F:THR197 4.1 47.2 1.0
SG F:CYS221 4.2 30.9 1.0
CB F:CYS221 4.2 28.9 1.0
NE2 F:HIS118 4.2 43.9 1.0
CD2 F:HIS118 4.2 41.5 1.0
ND1 F:HIS116 4.3 28.5 0.6
HG21 F:THR197 4.3 47.2 1.0
CG F:ASP120 4.5 29.4 1.0
CG F:HIS116 4.5 31.0 0.6
CG F:HIS116 4.6 30.3 0.4
CG2 F:THR197 4.7 39.4 1.0
ND1 F:HIS116 4.7 28.0 0.4
HD2 F:TYR233 4.7 54.5 1.0
H F:HIS118 4.8 40.4 1.0
CA F:HIS118 4.9 34.4 1.0
NE2 F:HIS263 4.9 28.9 1.0

Zinc binding site 6 out of 6 in 5mmd

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Zinc binding site 6 out of 6 in the Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tmb-1. Structural Insights Into Tmb-1 and the Role of Residue 119 and 228 in Substrate and Inhibitor Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:15.6
occ:0.30
ZN F:ZN402 0.0 15.6 0.3
NE2 F:HIS116 1.4 40.8 0.6
ZN F:ZN402 1.5 18.4 0.7
ND1 F:HIS118 1.8 39.8 1.0
HD2 F:HIS116 2.0 39.6 0.4
NE2 F:HIS116 2.1 29.8 0.4
CD2 F:HIS116 2.2 33.7 0.6
CD2 F:HIS116 2.2 33.0 0.4
HD2 F:HIS116 2.3 40.4 0.6
CG F:HIS118 2.3 38.8 1.0
HB2 F:HIS118 2.4 42.5 1.0
NE2 F:HIS196 2.6 36.1 1.0
CE1 F:HIS116 2.6 30.8 0.6
CE1 F:HIS118 2.6 42.6 1.0
HD2 F:HIS196 2.8 43.6 1.0
CB F:HIS118 2.9 35.4 1.0
HE1 F:HIS116 3.0 37.0 0.6
CD2 F:HIS196 3.0 36.4 1.0
HG21 F:THR197 3.1 47.2 1.0
HE1 F:HIS118 3.1 51.2 1.0
O F:HOH510 3.2 31.4 1.0
CD2 F:HIS118 3.2 41.5 1.0
CE1 F:HIS116 3.3 28.3 0.4
HB3 F:HIS118 3.4 42.5 1.0
CG F:HIS116 3.4 31.0 0.6
NE2 F:HIS118 3.4 43.9 1.0
HG23 F:THR197 3.4 47.2 1.0
ND1 F:HIS116 3.5 28.5 0.6
CG F:HIS116 3.5 30.3 0.4
H F:HIS118 3.5 40.4 1.0
CG2 F:THR197 3.7 39.4 1.0
CE1 F:HIS196 3.8 37.0 1.0
O F:HOH595 3.8 44.8 1.0
HE1 F:HIS116 3.9 34.0 0.4
HD2 F:HIS118 4.0 49.8 1.0
ND1 F:HIS116 4.0 28.0 0.4
HG1 F:THR197 4.1 43.6 1.0
CA F:HIS118 4.1 34.4 1.0
N F:HIS118 4.2 33.6 1.0
HE1 F:HIS196 4.2 44.4 1.0
HG22 F:THR197 4.3 47.2 1.0
HB2 F:CYS221 4.3 34.7 1.0
CG F:HIS196 4.3 36.9 1.0
ZN F:ZN401 4.4 43.7 1.0
OD1 F:ASP120 4.4 30.3 1.0
OG1 F:THR197 4.5 36.4 1.0
HB2 F:HIS116 4.6 37.2 0.4
HA F:HIS118 4.6 41.3 1.0
ND1 F:HIS196 4.7 37.5 1.0
CB F:HIS116 4.7 31.0 0.4
CB F:HIS116 4.7 31.0 0.6
CB F:THR197 4.8 39.6 1.0
HB2 F:HIS116 4.8 37.2 0.6
HB3 F:CYS221 4.9 34.7 1.0
CB F:CYS221 4.9 28.9 1.0
SG F:CYS221 4.9 30.9 1.0
OD2 F:ASP120 5.0 30.6 1.0

Reference:

S.Skagseth, T.Christopeit, S.Akhter, A.Bayer, H.S.Leiros. Structural Insights Into Tmb-1 and the Role of Residues 119 and 228 in Substrate and Inhibitor Binding. Antimicrob. Agents V. 61 2017CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 28559248
DOI: 10.1128/AAC.02602-16
Page generated: Wed Dec 16 06:33:22 2020

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