Iron in PDB 6vzy: Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor
Protein crystallography data
The structure of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor, PDB code: 6vzy
was solved by
M.J.Mcbride,
A.K.Boal,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.42 /
1.66
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.953,
105.848,
150.591,
90,
90,
90
|
R / Rfree (%)
|
19 /
22.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor
(pdb code 6vzy). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor, PDB code: 6vzy:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 6vzy
Go back to
Iron Binding Sites List in 6vzy
Iron binding site 1 out
of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:12.2
occ:0.93
|
OE2
|
A:GLU215
|
2.1
|
19.0
|
1.0
|
ND1
|
A:HIS225
|
2.1
|
10.0
|
1.0
|
NE2
|
A:HIS311
|
2.1
|
10.4
|
1.0
|
O
|
A:HOH743
|
2.2
|
19.8
|
1.0
|
OE2
|
A:GLU189
|
2.2
|
21.3
|
1.0
|
OE1
|
A:GLU189
|
2.2
|
14.4
|
1.0
|
CD
|
A:GLU189
|
2.5
|
19.6
|
1.0
|
CE1
|
A:HIS225
|
2.9
|
17.2
|
1.0
|
CE1
|
A:HIS311
|
3.0
|
16.8
|
1.0
|
CD2
|
A:HIS311
|
3.1
|
18.4
|
1.0
|
CD
|
A:GLU215
|
3.2
|
19.9
|
1.0
|
CG
|
A:HIS225
|
3.2
|
11.7
|
1.0
|
CB
|
A:HIS225
|
3.7
|
15.2
|
1.0
|
CG
|
A:GLU189
|
4.0
|
19.1
|
1.0
|
O
|
A:HOH667
|
4.0
|
20.1
|
1.0
|
OE1
|
A:GLU215
|
4.0
|
19.5
|
1.0
|
CG
|
A:GLU215
|
4.0
|
13.3
|
1.0
|
CB
|
A:GLU215
|
4.0
|
12.3
|
1.0
|
O
|
A:HOH760
|
4.0
|
26.2
|
1.0
|
NE2
|
A:HIS225
|
4.1
|
14.8
|
1.0
|
ND1
|
A:HIS311
|
4.2
|
12.4
|
1.0
|
CA
|
A:GLU215
|
4.2
|
10.8
|
1.0
|
CG
|
A:HIS311
|
4.2
|
15.7
|
1.0
|
CD2
|
A:HIS225
|
4.3
|
16.2
|
1.0
|
OH
|
A:TYR307
|
4.5
|
13.1
|
1.0
|
O
|
A:GLU215
|
4.8
|
12.8
|
1.0
|
CB
|
A:GLU189
|
5.0
|
12.9
|
1.0
|
CE2
|
A:TYR307
|
5.0
|
10.2
|
1.0
|
|
Iron binding site 2 out
of 6 in 6vzy
Go back to
Iron Binding Sites List in 6vzy
Iron binding site 2 out
of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:11.4
occ:0.67
|
OE1
|
A:GLU281
|
2.0
|
22.9
|
1.0
|
OD1
|
A:ASP315
|
2.0
|
26.4
|
1.0
|
OE1
|
A:GLU215
|
2.0
|
19.5
|
1.0
|
ND1
|
A:HIS318
|
2.1
|
13.9
|
1.0
|
O
|
A:HOH667
|
2.1
|
20.1
|
1.0
|
CE1
|
A:HIS318
|
2.9
|
18.8
|
1.0
|
CD
|
A:GLU281
|
3.1
|
25.9
|
1.0
|
CG
|
A:ASP315
|
3.1
|
33.2
|
1.0
|
CD
|
A:GLU215
|
3.2
|
19.9
|
1.0
|
CG
|
A:HIS318
|
3.2
|
18.2
|
1.0
|
OE2
|
A:GLU281
|
3.4
|
22.8
|
1.0
|
OD2
|
A:ASP315
|
3.5
|
22.5
|
1.0
|
OE2
|
A:GLU215
|
3.6
|
19.0
|
1.0
|
CB
|
A:HIS318
|
3.7
|
19.8
|
1.0
|
NE2
|
A:HIS318
|
4.1
|
20.6
|
1.0
|
CD2
|
A:HIS318
|
4.3
|
23.2
|
1.0
|
CG1
|
A:VAL211
|
4.3
|
15.4
|
1.0
|
CG
|
A:GLU281
|
4.4
|
18.7
|
1.0
|
CB
|
A:ASP315
|
4.4
|
17.9
|
1.0
|
CG
|
A:GLU215
|
4.5
|
13.3
|
1.0
|
O
|
A:HOH743
|
4.5
|
19.8
|
1.0
|
CA
|
A:ASP315
|
4.7
|
22.3
|
1.0
|
CD2
|
A:HIS311
|
4.7
|
18.4
|
1.0
|
CG2
|
A:ILE314
|
4.9
|
34.0
|
1.0
|
CB
|
A:GLU281
|
5.0
|
19.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 6vzy
Go back to
Iron Binding Sites List in 6vzy
Iron binding site 3 out
of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:16.0
occ:1.00
|
NE2
|
A:HIS409
|
2.2
|
13.2
|
1.0
|
NE2
|
A:HIS407
|
2.2
|
11.3
|
1.0
|
NE2
|
A:HIS448
|
2.2
|
10.7
|
1.0
|
O
|
A:HOH780
|
2.3
|
20.1
|
1.0
|
CE1
|
A:HIS409
|
3.1
|
11.1
|
1.0
|
CD2
|
A:HIS407
|
3.1
|
16.3
|
1.0
|
CE1
|
A:HIS407
|
3.2
|
15.4
|
1.0
|
CE1
|
A:HIS448
|
3.2
|
14.6
|
1.0
|
CD2
|
A:HIS448
|
3.2
|
10.1
|
1.0
|
CD2
|
A:HIS409
|
3.2
|
11.1
|
1.0
|
O
|
A:HOH771
|
4.0
|
27.4
|
1.0
|
OE2
|
A:GLU413
|
4.2
|
26.7
|
1.0
|
ND1
|
A:HIS409
|
4.3
|
16.6
|
1.0
|
ND1
|
A:HIS407
|
4.3
|
9.8
|
1.0
|
CG
|
A:HIS407
|
4.3
|
10.2
|
1.0
|
ND1
|
A:HIS448
|
4.3
|
10.8
|
1.0
|
CG
|
A:HIS409
|
4.3
|
12.4
|
1.0
|
CG
|
A:HIS448
|
4.3
|
8.3
|
1.0
|
O
|
A:HOH782
|
4.6
|
29.4
|
1.0
|
CD1
|
A:ILE442
|
4.9
|
16.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 6vzy
Go back to
Iron Binding Sites List in 6vzy
Iron binding site 4 out
of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:13.2
occ:1.00
|
O
|
B:HOH719
|
2.1
|
16.3
|
1.0
|
OE2
|
B:GLU189
|
2.1
|
16.6
|
1.0
|
NE2
|
B:HIS311
|
2.1
|
11.9
|
1.0
|
ND1
|
B:HIS225
|
2.1
|
10.7
|
1.0
|
OE2
|
B:GLU215
|
2.2
|
14.4
|
1.0
|
OE1
|
B:GLU189
|
2.3
|
15.9
|
1.0
|
CD
|
B:GLU189
|
2.5
|
16.7
|
1.0
|
CE1
|
B:HIS225
|
2.9
|
12.0
|
1.0
|
CE1
|
B:HIS311
|
3.0
|
14.1
|
1.0
|
CD2
|
B:HIS311
|
3.1
|
17.3
|
1.0
|
CG
|
B:HIS225
|
3.2
|
9.0
|
1.0
|
CD
|
B:GLU215
|
3.3
|
18.7
|
1.0
|
CB
|
B:HIS225
|
3.7
|
10.0
|
1.0
|
CG
|
B:GLU189
|
3.9
|
13.4
|
1.0
|
CB
|
B:GLU215
|
4.0
|
13.4
|
1.0
|
O
|
B:HOH677
|
4.0
|
17.8
|
1.0
|
CG
|
B:GLU215
|
4.1
|
12.5
|
1.0
|
NE2
|
B:HIS225
|
4.1
|
15.7
|
1.0
|
OE1
|
B:GLU215
|
4.1
|
17.6
|
1.0
|
ND1
|
B:HIS311
|
4.1
|
14.1
|
1.0
|
CG
|
B:HIS311
|
4.2
|
12.1
|
1.0
|
O
|
B:HOH777
|
4.2
|
21.8
|
1.0
|
CD2
|
B:HIS225
|
4.3
|
13.3
|
1.0
|
CA
|
B:GLU215
|
4.3
|
12.7
|
1.0
|
O
|
B:HOH793
|
4.3
|
24.4
|
1.0
|
OH
|
B:TYR307
|
4.5
|
12.1
|
1.0
|
O
|
B:GLU215
|
4.8
|
12.2
|
1.0
|
CE1
|
B:TYR307
|
4.9
|
12.5
|
1.0
|
CB
|
B:GLU189
|
5.0
|
10.7
|
1.0
|
FE
|
B:FE2502
|
5.0
|
14.6
|
0.8
|
|
Iron binding site 5 out
of 6 in 6vzy
Go back to
Iron Binding Sites List in 6vzy
Iron binding site 5 out
of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:14.6
occ:0.84
|
OE1
|
B:GLU281
|
2.0
|
20.1
|
1.0
|
OD1
|
B:ASP315
|
2.0
|
22.2
|
1.0
|
OE1
|
B:GLU215
|
2.1
|
17.6
|
1.0
|
O
|
B:HOH677
|
2.1
|
17.8
|
1.0
|
ND1
|
B:HIS318
|
2.2
|
17.2
|
1.0
|
CD
|
B:GLU281
|
3.0
|
22.0
|
1.0
|
CE1
|
B:HIS318
|
3.1
|
21.9
|
1.0
|
CG
|
B:ASP315
|
3.1
|
22.9
|
1.0
|
CD
|
B:GLU215
|
3.2
|
18.7
|
1.0
|
CG
|
B:HIS318
|
3.3
|
20.8
|
1.0
|
OE2
|
B:GLU281
|
3.4
|
21.2
|
1.0
|
OE2
|
B:GLU215
|
3.5
|
14.4
|
1.0
|
OD2
|
B:ASP315
|
3.6
|
23.4
|
1.0
|
CB
|
B:HIS318
|
3.7
|
16.3
|
1.0
|
NE2
|
B:HIS318
|
4.3
|
26.3
|
1.0
|
CG1
|
B:VAL211
|
4.3
|
15.7
|
1.0
|
CG
|
B:GLU281
|
4.3
|
19.7
|
1.0
|
CD2
|
B:HIS318
|
4.4
|
22.5
|
1.0
|
O
|
B:HOH719
|
4.4
|
16.3
|
1.0
|
CB
|
B:ASP315
|
4.4
|
18.3
|
1.0
|
CG
|
B:GLU215
|
4.5
|
12.5
|
1.0
|
CA
|
B:ASP315
|
4.6
|
19.7
|
1.0
|
CD2
|
B:HIS311
|
4.7
|
17.3
|
1.0
|
CG2
|
B:ILE314
|
4.8
|
29.3
|
1.0
|
CB
|
B:GLU281
|
4.9
|
15.9
|
1.0
|
FE
|
B:FE2501
|
5.0
|
13.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 6vzy
Go back to
Iron Binding Sites List in 6vzy
Iron binding site 6 out
of 6 in the Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Sznf From Streptomyces Achromogenes Var. Streptozoticus Nrrl 2697 with A Diiron(II) Central Domain Cofactor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe503
b:17.4
occ:0.97
|
NE2
|
B:HIS409
|
2.2
|
16.3
|
1.0
|
NE2
|
B:HIS407
|
2.2
|
11.2
|
1.0
|
NE2
|
B:HIS448
|
2.2
|
11.7
|
1.0
|
O
|
B:HOH789
|
2.3
|
18.6
|
1.0
|
CD2
|
B:HIS409
|
3.1
|
16.1
|
1.0
|
CE1
|
B:HIS407
|
3.1
|
18.8
|
1.0
|
CD2
|
B:HIS448
|
3.2
|
12.6
|
1.0
|
CD2
|
B:HIS407
|
3.2
|
13.4
|
1.0
|
CE1
|
B:HIS448
|
3.2
|
9.0
|
1.0
|
CE1
|
B:HIS409
|
3.2
|
9.6
|
1.0
|
OE2
|
B:GLU413
|
4.2
|
23.6
|
1.0
|
ND1
|
B:HIS407
|
4.3
|
12.7
|
1.0
|
CG
|
B:HIS409
|
4.3
|
14.4
|
1.0
|
ND1
|
B:HIS448
|
4.3
|
9.1
|
1.0
|
CG
|
B:HIS448
|
4.3
|
11.0
|
1.0
|
ND1
|
B:HIS409
|
4.3
|
16.8
|
1.0
|
CG
|
B:HIS407
|
4.3
|
9.4
|
1.0
|
O
|
B:HOH796
|
4.4
|
24.5
|
1.0
|
CD1
|
B:ILE442
|
4.7
|
13.9
|
1.0
|
|
Reference:
M.J.Mcbride,
S.R.Pope,
K.Hu,
C.D.Okafor,
E.P.Balskus,
J.M.Bollinger Jr.,
A.K.Boal.
Structure and Assembly of the Diiron Cofactor in the Heme-Oxygenase-Like Domain of the N-Nitrosourea-Producing Enzyme Sznf Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490
Page generated: Wed Aug 7 13:46:19 2024
|