Manganese in PDB 2vqa: Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca.
Protein crystallography data
The structure of Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca., PDB code: 2vqa
was solved by
S.Tottey,
K.J.Waldron,
S.J.Firbank,
B.Reale,
C.Bessant,
K.Sato,
J.Gray,
M.J.Banfield,
C.Dennison,
N.J.Robinson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
58.32 /
2.95
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
236.190,
236.190,
134.041,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.1 /
23.3
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca.
(pdb code 2vqa). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca., PDB code: 2vqa:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 2vqa
Go back to
Manganese Binding Sites List in 2vqa
Manganese binding site 1 out
of 6 in the Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1005
b:12.4
occ:1.00
|
OE1
|
A:GLU108
|
1.9
|
12.4
|
1.0
|
NE2
|
A:HIS101
|
2.2
|
12.4
|
1.0
|
O
|
A:HOH2014
|
2.2
|
12.4
|
1.0
|
NE2
|
A:HIS147
|
2.3
|
12.4
|
1.0
|
NE2
|
A:HIS103
|
2.4
|
12.4
|
1.0
|
CE1
|
A:HIS101
|
3.0
|
12.4
|
1.0
|
CD
|
A:GLU108
|
3.0
|
12.4
|
1.0
|
CD2
|
A:HIS147
|
3.3
|
12.4
|
1.0
|
CD2
|
A:HIS101
|
3.3
|
12.4
|
1.0
|
CE1
|
A:HIS103
|
3.3
|
12.4
|
1.0
|
CE1
|
A:HIS147
|
3.3
|
12.4
|
1.0
|
CD2
|
A:HIS103
|
3.3
|
12.4
|
1.0
|
OE2
|
A:GLU108
|
3.4
|
12.4
|
1.0
|
ND1
|
A:HIS101
|
4.1
|
12.4
|
1.0
|
CG
|
A:HIS101
|
4.3
|
12.4
|
1.0
|
CG
|
A:GLU108
|
4.3
|
12.4
|
1.0
|
CG
|
A:HIS147
|
4.4
|
12.4
|
1.0
|
ND1
|
A:HIS147
|
4.4
|
12.4
|
1.0
|
ND1
|
A:HIS103
|
4.4
|
12.4
|
1.0
|
CG
|
A:HIS103
|
4.5
|
12.4
|
1.0
|
CE1
|
A:PHE163
|
4.5
|
12.4
|
1.0
|
CZ
|
A:PHE163
|
4.7
|
12.4
|
1.0
|
OE2
|
A:GLU170
|
4.7
|
12.4
|
1.0
|
CB
|
A:GLU108
|
4.8
|
12.4
|
1.0
|
CD2
|
A:PHE141
|
4.8
|
12.4
|
1.0
|
|
Manganese binding site 2 out
of 6 in 2vqa
Go back to
Manganese Binding Sites List in 2vqa
Manganese binding site 2 out
of 6 in the Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1006
b:12.4
occ:1.00
|
OE1
|
A:GLU290
|
2.0
|
12.4
|
1.0
|
NE2
|
A:HIS283
|
2.2
|
12.4
|
1.0
|
O
|
A:ACT1395
|
2.3
|
12.4
|
1.0
|
NE2
|
A:HIS285
|
2.3
|
12.4
|
1.0
|
NE2
|
A:HIS329
|
2.4
|
12.4
|
1.0
|
CD
|
A:GLU290
|
2.9
|
12.4
|
1.0
|
OE2
|
A:GLU290
|
3.0
|
12.4
|
1.0
|
CE1
|
A:HIS283
|
3.1
|
12.4
|
1.0
|
CE1
|
A:HIS285
|
3.2
|
12.4
|
1.0
|
CE1
|
A:HIS329
|
3.3
|
12.4
|
1.0
|
C
|
A:ACT1395
|
3.3
|
12.4
|
1.0
|
CD2
|
A:HIS283
|
3.3
|
12.4
|
1.0
|
CD2
|
A:HIS329
|
3.3
|
12.4
|
1.0
|
CD2
|
A:HIS285
|
3.3
|
12.4
|
1.0
|
OXT
|
A:ACT1395
|
3.6
|
12.4
|
1.0
|
ND1
|
A:HIS283
|
4.3
|
12.4
|
1.0
|
CG
|
A:GLU290
|
4.3
|
12.4
|
1.0
|
ND1
|
A:HIS285
|
4.3
|
12.4
|
1.0
|
ND1
|
A:HIS329
|
4.4
|
12.4
|
1.0
|
CG
|
A:HIS283
|
4.4
|
12.4
|
1.0
|
CG
|
A:HIS329
|
4.4
|
12.4
|
1.0
|
CG
|
A:HIS285
|
4.4
|
12.4
|
1.0
|
CE1
|
A:PHE345
|
4.5
|
12.4
|
1.0
|
CH3
|
A:ACT1395
|
4.6
|
12.4
|
1.0
|
CZ
|
A:PHE345
|
4.6
|
12.4
|
1.0
|
CB
|
A:GLU290
|
4.8
|
12.4
|
1.0
|
NH1
|
A:ARG280
|
4.8
|
12.4
|
1.0
|
|
Manganese binding site 3 out
of 6 in 2vqa
Go back to
Manganese Binding Sites List in 2vqa
Manganese binding site 3 out
of 6 in the Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1001
b:12.4
occ:1.00
|
OE1
|
B:GLU108
|
2.1
|
12.4
|
1.0
|
O
|
B:HOH2008
|
2.1
|
12.4
|
1.0
|
NE2
|
B:HIS101
|
2.2
|
12.4
|
1.0
|
NE2
|
B:HIS147
|
2.4
|
12.4
|
1.0
|
NE2
|
B:HIS103
|
2.4
|
12.4
|
1.0
|
CE1
|
B:HIS101
|
3.0
|
12.4
|
1.0
|
CD
|
B:GLU108
|
3.0
|
12.4
|
1.0
|
CD2
|
B:HIS147
|
3.1
|
12.4
|
1.0
|
OE2
|
B:GLU108
|
3.2
|
12.4
|
1.0
|
CE1
|
B:HIS103
|
3.2
|
12.4
|
1.0
|
CD2
|
B:HIS101
|
3.2
|
12.4
|
1.0
|
CD2
|
B:HIS103
|
3.5
|
12.4
|
1.0
|
CE1
|
B:HIS147
|
3.5
|
12.4
|
1.0
|
ND1
|
B:HIS101
|
4.2
|
12.4
|
1.0
|
CG
|
B:HIS101
|
4.3
|
12.4
|
1.0
|
CG
|
B:HIS147
|
4.4
|
12.4
|
1.0
|
ND1
|
B:HIS103
|
4.4
|
12.4
|
1.0
|
CG
|
B:GLU108
|
4.4
|
12.4
|
1.0
|
CE1
|
B:PHE163
|
4.5
|
12.4
|
1.0
|
ND1
|
B:HIS147
|
4.5
|
12.4
|
1.0
|
CG
|
B:HIS103
|
4.5
|
12.4
|
1.0
|
OE2
|
B:GLU170
|
4.6
|
12.4
|
1.0
|
CZ
|
B:PHE163
|
4.7
|
12.4
|
1.0
|
CB
|
B:GLU108
|
4.9
|
12.4
|
1.0
|
CD2
|
B:PHE141
|
4.9
|
12.4
|
1.0
|
|
Manganese binding site 4 out
of 6 in 2vqa
Go back to
Manganese Binding Sites List in 2vqa
Manganese binding site 4 out
of 6 in the Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1002
b:12.4
occ:1.00
|
OE1
|
B:GLU290
|
2.0
|
12.4
|
1.0
|
O
|
B:ACT1395
|
2.3
|
12.4
|
1.0
|
NE2
|
B:HIS285
|
2.3
|
12.4
|
1.0
|
NE2
|
B:HIS283
|
2.3
|
12.4
|
1.0
|
NE2
|
B:HIS329
|
2.4
|
12.4
|
1.0
|
CD
|
B:GLU290
|
3.0
|
12.4
|
1.0
|
CE1
|
B:HIS285
|
3.1
|
12.4
|
1.0
|
CE1
|
B:HIS283
|
3.1
|
12.4
|
1.0
|
C
|
B:ACT1395
|
3.2
|
12.4
|
1.0
|
OE2
|
B:GLU290
|
3.2
|
12.4
|
1.0
|
CE1
|
B:HIS329
|
3.3
|
12.4
|
1.0
|
CD2
|
B:HIS283
|
3.3
|
12.4
|
1.0
|
CD2
|
B:HIS329
|
3.3
|
12.4
|
1.0
|
CD2
|
B:HIS285
|
3.3
|
12.4
|
1.0
|
OXT
|
B:ACT1395
|
3.3
|
12.4
|
1.0
|
ND1
|
B:HIS285
|
4.3
|
12.4
|
1.0
|
ND1
|
B:HIS283
|
4.3
|
12.4
|
1.0
|
CZ
|
B:PHE345
|
4.3
|
12.4
|
1.0
|
CG
|
B:GLU290
|
4.4
|
12.4
|
1.0
|
CG
|
B:HIS283
|
4.4
|
12.4
|
1.0
|
ND1
|
B:HIS329
|
4.4
|
12.4
|
1.0
|
CG
|
B:HIS285
|
4.4
|
12.4
|
1.0
|
CG
|
B:HIS329
|
4.5
|
12.4
|
1.0
|
CE1
|
B:PHE345
|
4.5
|
12.4
|
1.0
|
CH3
|
B:ACT1395
|
4.5
|
12.4
|
1.0
|
NH2
|
B:ARG280
|
4.7
|
12.4
|
1.0
|
CB
|
B:GLU290
|
4.8
|
12.4
|
1.0
|
|
Manganese binding site 5 out
of 6 in 2vqa
Go back to
Manganese Binding Sites List in 2vqa
Manganese binding site 5 out
of 6 in the Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn1003
b:12.4
occ:1.00
|
OE1
|
C:GLU108
|
1.8
|
12.4
|
1.0
|
O
|
C:HOH2010
|
2.1
|
12.4
|
1.0
|
NE2
|
C:HIS101
|
2.2
|
12.4
|
1.0
|
NE2
|
C:HIS147
|
2.3
|
12.4
|
1.0
|
NE2
|
C:HIS103
|
2.4
|
12.4
|
1.0
|
CD
|
C:GLU108
|
2.8
|
12.4
|
1.0
|
CE1
|
C:HIS101
|
3.0
|
12.4
|
1.0
|
CD2
|
C:HIS147
|
3.1
|
12.4
|
1.0
|
OE2
|
C:GLU108
|
3.2
|
12.4
|
1.0
|
CD2
|
C:HIS101
|
3.3
|
12.4
|
1.0
|
CE1
|
C:HIS147
|
3.3
|
12.4
|
1.0
|
CE1
|
C:HIS103
|
3.4
|
12.4
|
1.0
|
CD2
|
C:HIS103
|
3.4
|
12.4
|
1.0
|
ND1
|
C:HIS101
|
4.2
|
12.4
|
1.0
|
CG
|
C:GLU108
|
4.2
|
12.4
|
1.0
|
CG
|
C:HIS147
|
4.3
|
12.4
|
1.0
|
CG
|
C:HIS101
|
4.4
|
12.4
|
1.0
|
ND1
|
C:HIS147
|
4.4
|
12.4
|
1.0
|
OE1
|
C:GLU170
|
4.4
|
12.4
|
1.0
|
ND1
|
C:HIS103
|
4.5
|
12.4
|
1.0
|
CG
|
C:HIS103
|
4.5
|
12.4
|
1.0
|
CE1
|
C:PHE163
|
4.6
|
12.4
|
1.0
|
CB
|
C:GLU108
|
4.7
|
12.4
|
1.0
|
CZ
|
C:PHE163
|
4.8
|
12.4
|
1.0
|
CD2
|
C:PHE141
|
5.0
|
12.4
|
1.0
|
|
Manganese binding site 6 out
of 6 in 2vqa
Go back to
Manganese Binding Sites List in 2vqa
Manganese binding site 6 out
of 6 in the Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Protein-Folding Location Can Regulate Mn Versus Cu- or Zn- Binding. Crystal Structure of Mnca. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn1004
b:12.4
occ:1.00
|
OE1
|
C:GLU290
|
2.1
|
12.4
|
1.0
|
NE2
|
C:HIS283
|
2.2
|
12.4
|
1.0
|
NE2
|
C:HIS285
|
2.3
|
12.4
|
1.0
|
NE2
|
C:HIS329
|
2.3
|
12.4
|
1.0
|
OXT
|
C:ACT1393
|
2.5
|
12.4
|
1.0
|
CD
|
C:GLU290
|
3.0
|
12.4
|
1.0
|
CE1
|
C:HIS283
|
3.0
|
12.4
|
1.0
|
OE2
|
C:GLU290
|
3.1
|
12.4
|
1.0
|
CE1
|
C:HIS329
|
3.2
|
12.4
|
1.0
|
CE1
|
C:HIS285
|
3.2
|
12.4
|
1.0
|
O
|
C:ACT1393
|
3.2
|
12.4
|
1.0
|
C
|
C:ACT1393
|
3.3
|
12.4
|
1.0
|
CD2
|
C:HIS285
|
3.3
|
12.4
|
1.0
|
CD2
|
C:HIS329
|
3.3
|
12.4
|
1.0
|
CD2
|
C:HIS283
|
3.4
|
12.4
|
1.0
|
ND1
|
C:HIS283
|
4.2
|
12.4
|
1.0
|
ND1
|
C:HIS329
|
4.3
|
12.4
|
1.0
|
ND1
|
C:HIS285
|
4.4
|
12.4
|
1.0
|
CG
|
C:GLU290
|
4.4
|
12.4
|
1.0
|
CG
|
C:HIS329
|
4.4
|
12.4
|
1.0
|
CG
|
C:HIS283
|
4.4
|
12.4
|
1.0
|
CG
|
C:HIS285
|
4.4
|
12.4
|
1.0
|
CE1
|
C:PHE345
|
4.5
|
12.4
|
1.0
|
CZ
|
C:PHE345
|
4.5
|
12.4
|
1.0
|
NH2
|
C:ARG280
|
4.7
|
12.4
|
1.0
|
CH3
|
C:ACT1393
|
4.7
|
12.4
|
1.0
|
CB
|
C:GLU290
|
4.9
|
12.4
|
1.0
|
|
Reference:
S.Tottey,
K.J.Waldron,
S.J.Firbank,
B.Reale,
C.Bessant,
K.Sato,
T.R.Cheek,
J.Gray,
M.J.Banfield,
C.Dennison,
N.J.Robinson.
Protein-Folding Location Can Regulate Manganese-Binding Versus Copper- or Zinc-Binding. Nature V. 455 1138 2008.
ISSN: ISSN 0028-0836
PubMed: 18948958
DOI: 10.1038/NATURE07340
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