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: Thu Oct 17 02:18:19 2024
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