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Zinc in PDB 4j4m: Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase

Enzymatic activity of Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase

All present enzymatic activity of Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase:
3.4.24.53;

Protein crystallography data

The structure of Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase, PDB code: 4j4m was solved by T.L.Chou, C.H.Wu, K.F.Huang, A.H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 80.766, 80.766, 120.451, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 20.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase (pdb code 4j4m). 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 Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase, PDB code: 4j4m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4j4m

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Zinc binding site 1 out of 6 in the Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase


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 Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:28.0
occ:1.00
 NE2 A:HIS154 2.0 32.5 1.0
NE2 A:HIS148 2.0 26.2 1.0
NE2 A:HIS144 2.1 25.4 1.0
O A:HOH401 2.2 30.0 1.0
CD2 A:HIS154 3.0 34.4 1.0
CE1 A:HIS148 3.0 28.2 1.0
CD2 A:HIS144 3.0 23.6 1.0
CD2 A:HIS148 3.1 25.5 1.0
CE1 A:HIS154 3.1 34.1 1.0
CE1 A:HIS144 3.2 24.2 1.0
ND1 A:HIS148 4.1 28.3 1.0
ND1 A:HIS154 4.2 35.6 1.0
CG A:HIS154 4.2 35.0 1.0
CG A:HIS148 4.2 25.7 1.0
CG A:HIS144 4.2 23.0 1.0
ND1 A:HIS144 4.3 23.1 1.0
O A:HOH412 4.4 28.2 1.0
O A:HOH424 4.5 59.6 1.0
O A:HOH524 4.6 47.2 1.0
OE1 A:GLU145 4.7 20.4 1.0
CE A:MET167 4.7 27.9 1.0
OE2 A:GLU145 4.8 21.2 1.0

Zinc binding site 2 out of 6 in 4j4m

Go back to Zinc Binding Sites List in 4j4m
Zinc binding site 2 out of 6 in the Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase


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 Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:34.4
occ:1.00
 O A:HOH638 1.8 18.0 1.0
NE2 A:HIS18 2.0 25.0 1.0
O A:HOH629 2.3 30.5 1.0
O A:HOH593 2.4 32.5 1.0
CE1 A:HIS18 2.8 27.1 1.0
CD2 A:HIS18 3.2 26.6 1.0
ND1 A:HIS18 4.0 27.6 1.0
O A:SER62 4.2 25.7 1.0
CG A:HIS18 4.2 23.9 1.0
OG1 A:THR22 4.3 22.7 1.0
O A:SER63 4.6 28.4 1.0
O A:HOH605 4.6 42.5 1.0

Zinc binding site 3 out of 6 in 4j4m

Go back to Zinc Binding Sites List in 4j4m
Zinc binding site 3 out of 6 in the Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase


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 Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:51.7
occ:1.00
 O A:PRO203 4.1 37.3 1.0
O A:ALA202 4.5 32.5 1.0
OXT A:PRO203 4.5 39.2 1.0
C A:PRO203 4.6 37.1 1.0

Zinc binding site 4 out of 6 in 4j4m

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Zinc binding site 4 out of 6 in the Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase


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 Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:24.0
occ:1.00
 OD1 A:ASP106 2.0 23.9 1.0
OD1 A:ASP72 2.1 23.8 1.0
CG A:ASP106 2.9 22.6 1.0
CG A:ASP72 3.0 24.0 1.0
OD2 A:ASP106 3.1 22.9 1.0
CB A:ASP72 3.3 23.7 1.0
CA A:ASP72 3.9 22.4 1.0
OD2 A:ASP72 4.1 24.5 1.0
O A:HOH507 4.1 20.5 1.0
CB A:ASP106 4.3 23.0 1.0
O A:HOH479 4.5 20.3 1.0
N A:ASP72 4.8 23.0 1.0

Zinc binding site 5 out of 6 in 4j4m

Go back to Zinc Binding Sites List in 4j4m
Zinc binding site 5 out of 6 in the Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase


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 Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:24.7
occ:1.00
 NE2 B:HIS154 1.9 25.2 1.0
NE2 B:HIS144 2.1 20.8 1.0
NE2 B:HIS148 2.1 18.7 1.0
O B:HOH423 2.7 27.5 1.0
CD2 B:HIS154 2.9 26.4 1.0
CE1 B:HIS154 2.9 26.4 1.0
CD2 B:HIS144 2.9 21.1 1.0
CD2 B:HIS148 3.1 19.2 1.0
CE1 B:HIS148 3.1 22.5 1.0
CE1 B:HIS144 3.2 20.6 1.0
ND1 B:HIS154 4.0 27.6 1.0
CG B:HIS154 4.0 27.9 1.0
CG B:HIS144 4.1 19.7 1.0
ND1 B:HIS144 4.2 20.8 1.0
ND1 B:HIS148 4.2 21.9 1.0
CG B:HIS148 4.2 19.2 1.0
O B:HOH570 4.2 50.5 1.0
O B:HOH555 4.3 20.1 1.0
O B:HOH659 4.6 62.5 1.0
O B:HOH670 4.7 49.2 1.0
CE B:MET167 4.7 21.6 1.0
OE1 B:GLU145 4.7 23.4 1.0
OE2 B:GLU145 4.7 23.8 1.0

Zinc binding site 6 out of 6 in 4j4m

Go back to Zinc Binding Sites List in 4j4m
Zinc binding site 6 out of 6 in the Crystal Structure of Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase


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 Tm-1, A Trimeresurus Mucrosquamatus Venom Metalloproteinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:25.0
occ:1.00
 OD1 B:ASP106 2.0 23.8 1.0
OD1 B:ASP72 2.2 20.9 1.0
CG B:ASP106 2.9 23.9 1.0
CG B:ASP72 3.0 21.2 1.0
OD2 B:ASP106 3.2 23.1 1.0
CB B:ASP72 3.4 20.7 1.0
CA B:ASP72 4.0 20.2 1.0
OD2 B:ASP72 4.1 21.9 1.0
CB B:ASP106 4.3 24.8 1.0
O B:HOH502 4.4 24.5 1.0
O B:HOH434 4.6 19.8 1.0
OD1 B:ASP107 4.8 41.0 1.0
O B:HOH548 4.8 21.4 1.0
O B:HOH620 4.8 28.9 1.0
N B:ASP72 4.9 20.0 1.0

Reference:

T.L.Chou, C.H.Wu, K.F.Huang, A.H.Wang. Crystal Structure of A Trimeresurus Mucrosquamatus Venom Metalloproteinase Providing New Insights Into the Inhibition By Endogenous Tripeptide Inhibitors. Toxicon V. 71C 140 2013.
ISSN: ISSN 0041-0101
PubMed: 23732127
DOI: 10.1016/J.TOXICON.2013.05.009
Page generated: Wed Dec 16 05:25:04 2020

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