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Zinc in PDB 2nvv: Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16.

Protein crystallography data

The structure of Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16., PDB code: 2nvv was solved by F.Forouhar, H.Neely, J.Seetharaman, W.Yong, C.K.Ho, Y.Fang, K.Cunningham, L.-C.Ma, R.Xiao, J.Liu, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.70
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 131.051, 131.051, 162.093, 90.00, 90.00, 120.00
R / Rfree (%) 28.7 / 29

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16. (pdb code 2nvv). 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 the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16., PDB code: 2nvv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2nvv

Go back to Zinc Binding Sites List in 2nvv
Zinc binding site 1 out of 6 in the Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16.


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 the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:16.9
occ:1.00
NE2 A:HIS417 2.1 6.6 1.0
O B:HOH526 2.4 4.8 1.0
NE2 B:HIS411 2.4 6.4 1.0
OD1 B:ASP413 2.5 6.4 1.0
OE1 A:GLU416 2.5 7.6 1.0
CE1 A:HIS417 3.0 6.4 1.0
CD2 A:HIS417 3.0 6.8 1.0
CE1 B:HIS411 3.3 6.4 1.0
CD2 B:HIS411 3.5 7.0 1.0
CD A:GLU416 3.5 6.9 1.0
CG B:ASP413 3.7 6.4 1.0
CG A:GLU416 3.7 6.5 1.0
OG1 B:THR365 3.8 6.4 1.0
ND1 A:HIS417 4.1 6.5 1.0
CG A:HIS417 4.1 7.0 1.0
O A:HOH518 4.2 19.4 1.0
OD2 B:ASP413 4.2 6.9 1.0
OD1 B:ASP102 4.3 6.4 1.0
O B:HIS412 4.5 6.4 1.0
ND1 B:HIS411 4.5 6.4 1.0
CE1 B:HIS366 4.5 7.3 1.0
CG B:HIS411 4.6 6.4 1.0
OE2 A:GLU416 4.6 7.1 1.0
ND1 B:HIS366 4.7 6.4 1.0
CB B:ASP413 4.8 6.4 1.0
CB B:THR365 4.8 6.4 1.0
CA B:ASP413 4.9 6.5 1.0
CG2 B:THR365 5.0 6.4 1.0

Zinc binding site 2 out of 6 in 2nvv

Go back to Zinc Binding Sites List in 2nvv
Zinc binding site 2 out of 6 in the Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16.


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 the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn507

b:20.6
occ:1.00
O A:HOH533 2.2 21.3 1.0
NE2 B:HIS417 2.2 6.6 1.0
NE2 A:HIS411 2.3 6.4 1.0
O A:HOH532 2.4 28.5 1.0
OE1 B:GLU416 2.5 7.6 1.0
OD1 A:ASP413 2.5 6.4 1.0
CD2 B:HIS417 3.1 6.8 1.0
CE1 A:HIS411 3.2 6.4 1.0
CE1 B:HIS417 3.2 6.4 1.0
CD2 A:HIS411 3.4 7.0 1.0
CD B:GLU416 3.4 6.9 1.0
CG A:ASP413 3.6 6.4 1.0
CG B:GLU416 3.7 6.5 1.0
OG1 A:THR365 3.8 6.4 1.0
OD2 A:ASP413 4.2 6.9 1.0
O A:HIS412 4.3 6.4 1.0
CG B:HIS417 4.3 7.0 1.0
ND1 B:HIS417 4.3 6.5 1.0
O B:HOH523 4.3 18.2 1.0
ND1 A:HIS411 4.3 6.4 1.0
CG A:HIS411 4.5 6.4 1.0
OD1 A:ASP102 4.5 6.4 1.0
CE1 A:HIS366 4.6 7.3 1.0
OE2 B:GLU416 4.6 7.1 1.0
ND1 A:HIS366 4.7 6.4 1.0
CB A:ASP413 4.8 6.4 1.0
CA A:ASP413 4.8 6.5 1.0
CB A:THR365 4.9 6.4 1.0
C A:HIS412 5.0 6.4 1.0

Zinc binding site 3 out of 6 in 2nvv

Go back to Zinc Binding Sites List in 2nvv
Zinc binding site 3 out of 6 in the Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16.


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 the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn507

b:18.5
occ:1.00
O C:HOH531 2.3 36.0 1.0
OD1 C:ASP413 2.3 6.4 1.0
NE2 D:HIS417 2.3 6.6 1.0
NE2 C:HIS411 2.4 6.4 1.0
O C:HOH530 2.7 34.6 1.0
OE1 D:GLU416 2.7 7.6 1.0
CD2 D:HIS417 3.2 6.8 1.0
CE1 C:HIS411 3.3 6.4 1.0
CE1 D:HIS417 3.3 6.4 1.0
CD2 C:HIS411 3.3 7.0 1.0
CG C:ASP413 3.5 6.4 1.0
OG1 C:THR365 3.6 6.4 1.0
CD D:GLU416 3.7 6.9 1.0
CG D:GLU416 3.9 6.5 1.0
OD2 C:ASP413 4.0 6.9 1.0
OD1 C:ASP102 4.3 6.4 1.0
O D:HOH526 4.3 34.3 1.0
ND1 D:HIS417 4.4 6.5 1.0
CG D:HIS417 4.4 7.0 1.0
ND1 C:HIS411 4.4 6.4 1.0
O C:HIS412 4.4 6.4 1.0
CE1 C:HIS366 4.4 7.3 1.0
CG C:HIS411 4.5 6.4 1.0
ND1 C:HIS366 4.6 6.4 1.0
CB C:THR365 4.6 6.4 1.0
CB C:ASP413 4.6 6.4 1.0
CA C:ASP413 4.8 6.5 1.0
CG2 C:THR365 4.8 6.4 1.0
OE2 D:GLU416 4.9 7.1 1.0

Zinc binding site 4 out of 6 in 2nvv

Go back to Zinc Binding Sites List in 2nvv
Zinc binding site 4 out of 6 in the Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16.


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 the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:17.7
occ:1.00
NE2 D:HIS411 2.2 6.4 1.0
O C:HOH508 2.4 3.5 1.0
OD1 D:ASP413 2.4 6.4 1.0
NE2 C:HIS417 2.5 6.6 1.0
OE1 C:GLU416 2.6 7.6 1.0
CE1 D:HIS411 3.1 6.4 1.0
CD2 D:HIS411 3.2 7.0 1.0
CD2 C:HIS417 3.4 6.8 1.0
CG D:ASP413 3.5 6.4 1.0
CE1 C:HIS417 3.5 6.4 1.0
OG1 D:THR365 3.5 6.4 1.0
CD C:GLU416 3.6 6.9 1.0
CG C:GLU416 3.9 6.5 1.0
OD2 D:ASP413 4.0 6.9 1.0
O C:HOH526 4.1 28.7 1.0
ND1 D:HIS411 4.3 6.4 1.0
CG D:HIS411 4.3 6.4 1.0
O D:HIS412 4.4 6.4 1.0
CE1 D:HIS366 4.4 7.3 1.0
OD1 D:ASP102 4.4 6.4 1.0
ND1 D:HIS366 4.5 6.4 1.0
ND1 C:HIS417 4.6 6.5 1.0
CG C:HIS417 4.6 7.0 1.0
CB D:ASP413 4.6 6.4 1.0
CB D:THR365 4.6 6.4 1.0
CA D:ASP413 4.8 6.5 1.0
OE2 C:GLU416 4.8 7.1 1.0
CG2 D:THR365 4.8 6.4 1.0

Zinc binding site 5 out of 6 in 2nvv

Go back to Zinc Binding Sites List in 2nvv
Zinc binding site 5 out of 6 in the Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16.


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 the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn507

b:15.7
occ:1.00
OD1 E:ASP413 2.2 6.4 1.0
NE2 E:HIS411 2.3 6.4 1.0
NE2 F:HIS417 2.4 6.6 1.0
O E:HOH544 2.6 25.5 1.0
OE1 F:GLU416 2.8 7.6 1.0
O E:HOH545 3.0 18.5 1.0
CD2 E:HIS411 3.2 7.0 1.0
CD2 F:HIS417 3.3 6.8 1.0
CE1 E:HIS411 3.3 6.4 1.0
CG E:ASP413 3.3 6.4 1.0
CE1 F:HIS417 3.4 6.4 1.0
OG1 E:THR365 3.5 6.4 1.0
CD F:GLU416 3.8 6.9 1.0
OD2 E:ASP413 3.9 6.9 1.0
CG F:GLU416 4.0 6.5 1.0
O E:HIS412 4.2 6.4 1.0
ND1 E:HIS411 4.4 6.4 1.0
CG E:HIS411 4.4 6.4 1.0
CG F:HIS417 4.4 7.0 1.0
OD1 E:ASP102 4.5 6.4 1.0
ND1 F:HIS417 4.5 6.5 1.0
CB E:ASP413 4.5 6.4 1.0
CE1 E:HIS366 4.5 7.3 1.0
CA E:ASP413 4.6 6.5 1.0
CB E:THR365 4.6 6.4 1.0
ND1 E:HIS366 4.7 6.4 1.0
CG2 E:THR365 4.8 6.4 1.0
C E:HIS412 4.9 6.4 1.0
OE2 F:GLU416 4.9 7.1 1.0

Zinc binding site 6 out of 6 in 2nvv

Go back to Zinc Binding Sites List in 2nvv
Zinc binding site 6 out of 6 in the Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16.


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 the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn508

b:25.7
occ:1.00
NE2 E:HIS417 2.2 6.6 1.0
NE2 F:HIS411 2.4 6.4 1.0
O F:HOH542 2.4 28.1 1.0
OD1 F:ASP413 2.4 6.4 1.0
OE1 E:GLU416 2.6 7.6 1.0
O F:HOH541 2.8 38.2 1.0
CD2 E:HIS417 3.1 6.8 1.0
CE1 E:HIS417 3.2 6.4 1.0
CE1 F:HIS411 3.3 6.4 1.0
CD2 F:HIS411 3.4 7.0 1.0
CD E:GLU416 3.5 6.9 1.0
CG F:ASP413 3.6 6.4 1.0
CG E:GLU416 3.7 6.5 1.0
OG1 F:THR365 3.8 6.4 1.0
OD2 F:ASP413 4.2 6.9 1.0
CG E:HIS417 4.2 7.0 1.0
ND1 E:HIS417 4.2 6.5 1.0
O F:HIS412 4.3 6.4 1.0
ND1 F:HIS411 4.4 6.4 1.0
OD1 F:ASP102 4.4 6.4 1.0
CG F:HIS411 4.5 6.4 1.0
CE1 F:HIS366 4.5 7.3 1.0
OE2 E:GLU416 4.7 7.1 1.0
ND1 F:HIS366 4.7 6.4 1.0
CB F:ASP413 4.8 6.4 1.0
CB F:THR365 4.8 6.4 1.0
CA F:ASP413 4.8 6.5 1.0
CG2 F:THR365 4.9 6.4 1.0

Reference:

F.Forouhar, H.Neely, J.Seetharaman, W.Yong, C.K.Ho, Y.Fang, K.Cunningham, L.-C.Ma, R.Xiao, J.Liu, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong. Crystal Structure of the Putative Acetyl-Coa Hydrolase/Transferase PG1013 From Porphyromonas Gingivalis, Northeast Structural Genomics Target PGR16 To Be Published.
Page generated: Wed Dec 16 03:44:29 2020

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