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Manganese in PDB 3p2u: Crystal Structure of Phnp in Complex with Orthovanadate

Protein crystallography data

The structure of Crystal Structure of Phnp in Complex with Orthovanadate, PDB code: 3p2u was solved by K.Podzelinska, Y.M.Kim, D.Zechel, F.Faucher, Z.Jia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.27 / 1.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.761, 75.285, 82.423, 90.00, 125.52, 90.00
R / Rfree (%) 16.1 / 18.6

Other elements in 3p2u:

The structure of Crystal Structure of Phnp in Complex with Orthovanadate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Vanadium (V) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Phnp in Complex with Orthovanadate (pdb code 3p2u). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Phnp in Complex with Orthovanadate, PDB code: 3p2u:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3p2u

Go back to Manganese Binding Sites List in 3p2u
Manganese binding site 1 out of 4 in the Crystal Structure of Phnp in Complex with Orthovanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Phnp in Complex with Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn260

b:16.0
occ:1.00
O A:HOH272 2.1 21.3 1.0
NE2 A:HIS143 2.1 19.3 1.0
ND1 A:HIS78 2.2 19.9 1.0
O1 A:VO4259 2.2 22.1 1.0
NE2 A:HIS76 2.2 14.5 1.0
OD2 A:ASP164 2.5 18.6 1.0
CE1 A:HIS78 3.0 21.1 1.0
CD2 A:HIS76 3.1 13.8 1.0
CE1 A:HIS143 3.1 19.6 1.0
CD2 A:HIS143 3.1 17.3 1.0
CG A:HIS78 3.2 16.5 1.0
CE1 A:HIS76 3.2 13.7 1.0
CG A:ASP164 3.5 20.9 1.0
V A:VO4259 3.5 54.7 1.0
MN A:MN261 3.5 18.9 0.8
CB A:HIS78 3.6 14.4 1.0
CB A:ASP164 3.9 22.1 1.0
O2 A:VO4259 4.0 33.8 1.0
O3 A:VO4259 4.2 37.1 1.0
NE2 A:HIS78 4.2 22.3 1.0
ND1 A:HIS143 4.2 21.2 1.0
CG A:HIS143 4.3 19.5 1.0
CG A:HIS76 4.3 13.2 1.0
NE2 A:HIS81 4.3 16.8 1.0
CD2 A:HIS78 4.3 21.1 1.0
ND1 A:HIS76 4.3 14.5 1.0
CD2 A:HIS81 4.4 15.0 1.0
OD1 A:ASP164 4.5 19.8 1.0
CE1 A:HIS200 4.6 20.3 1.0
OD1 A:ASP80 4.6 18.9 1.0
NE2 A:HIS200 4.9 21.3 1.0

Manganese binding site 2 out of 4 in 3p2u

Go back to Manganese Binding Sites List in 3p2u
Manganese binding site 2 out of 4 in the Crystal Structure of Phnp in Complex with Orthovanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Phnp in Complex with Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn261

b:18.9
occ:0.75
O2 A:VO4259 2.0 33.8 1.0
OD2 A:ASP164 2.2 18.6 1.0
NE2 A:HIS81 2.3 16.8 1.0
O A:HOH272 2.3 21.3 1.0
NE2 A:HIS222 2.4 22.5 1.0
OD2 A:ASP80 2.5 22.8 1.0
CG A:ASP164 3.0 20.9 1.0
OD1 A:ASP164 3.1 19.8 1.0
CD2 A:HIS81 3.1 15.0 1.0
CE1 A:HIS222 3.3 22.3 1.0
CE1 A:HIS81 3.4 14.7 1.0
CD2 A:HIS222 3.4 18.9 1.0
CG A:ASP80 3.4 18.2 1.0
V A:VO4259 3.5 54.7 1.0
OD1 A:ASP80 3.5 18.9 1.0
MN A:MN260 3.5 16.0 1.0
O A:HOH467 3.7 27.2 1.0
O1 A:VO4259 3.9 22.1 1.0
O A:HOH345 4.2 34.2 1.0
CE1 A:HIS200 4.2 20.3 1.0
NE2 A:HIS76 4.3 14.5 1.0
O3 A:VO4259 4.3 37.1 1.0
CG A:HIS81 4.4 14.4 1.0
CE1 A:HIS76 4.4 13.7 1.0
ND1 A:HIS81 4.4 13.9 1.0
CB A:ASP164 4.4 22.1 1.0
ND1 A:HIS222 4.5 24.4 1.0
CG A:HIS222 4.5 18.2 1.0
NE2 A:HIS200 4.8 21.3 1.0
CB A:ASP80 4.8 18.6 1.0
N A:ALA13 5.0 20.8 1.0
O4 A:VO4259 5.0 42.2 1.0

Manganese binding site 3 out of 4 in 3p2u

Go back to Manganese Binding Sites List in 3p2u
Manganese binding site 3 out of 4 in the Crystal Structure of Phnp in Complex with Orthovanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Phnp in Complex with Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn260

b:14.1
occ:0.80
O1 B:VO4259 2.0 21.5 0.8
O B:HOH277 2.2 18.8 1.0
OD2 B:ASP164 2.2 14.4 1.0
NE2 B:HIS81 2.2 13.3 1.0
NE2 B:HIS222 2.3 15.8 1.0
OD2 B:ASP80 2.4 17.1 1.0
CG B:ASP164 3.0 15.6 1.0
CD2 B:HIS81 3.1 15.3 1.0
OD1 B:ASP164 3.1 15.6 1.0
CE1 B:HIS222 3.2 16.4 1.0
CD2 B:HIS222 3.3 12.9 1.0
CG B:ASP80 3.3 15.6 1.0
CE1 B:HIS81 3.3 13.0 1.0
V B:VO4259 3.4 32.0 0.8
MN B:MN261 3.5 13.7 1.0
OD1 B:ASP80 3.6 16.8 1.0
O3 B:VO4259 3.8 14.5 0.8
O B:HOH321 4.0 22.0 1.0
O2 B:VO4259 4.2 21.1 0.8
CE1 B:HIS200 4.2 16.6 1.0
NE2 B:HIS76 4.3 13.8 1.0
CE1 B:HIS76 4.3 14.7 1.0
CG B:HIS81 4.3 13.4 1.0
ND1 B:HIS222 4.3 16.3 1.0
ND1 B:HIS81 4.4 12.4 1.0
O B:HOH371 4.4 28.3 1.0
CG B:HIS222 4.4 12.0 1.0
CB B:ASP164 4.4 16.6 1.0
CB B:ASP80 4.7 16.5 1.0
NE2 B:HIS200 4.9 17.3 1.0
O4 B:VO4259 4.9 26.7 0.8

Manganese binding site 4 out of 4 in 3p2u

Go back to Manganese Binding Sites List in 3p2u
Manganese binding site 4 out of 4 in the Crystal Structure of Phnp in Complex with Orthovanadate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Phnp in Complex with Orthovanadate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn261

b:13.7
occ:1.00
O3 B:VO4259 2.0 14.5 0.8
O B:HOH277 2.1 18.8 1.0
ND1 B:HIS78 2.1 17.1 1.0
NE2 B:HIS143 2.1 14.1 1.0
NE2 B:HIS76 2.2 13.8 1.0
OD2 B:ASP164 2.4 14.4 1.0
CE1 B:HIS78 3.0 17.9 1.0
CE1 B:HIS143 3.1 13.8 1.0
CD2 B:HIS76 3.1 12.1 1.0
CD2 B:HIS143 3.2 14.9 1.0
CE1 B:HIS76 3.2 14.7 1.0
CG B:HIS78 3.2 15.3 1.0
V B:VO4259 3.4 32.0 0.8
CG B:ASP164 3.4 15.6 1.0
MN B:MN260 3.5 14.1 0.8
CB B:HIS78 3.6 14.0 1.0
CB B:ASP164 3.9 16.6 1.0
O1 B:VO4259 3.9 21.5 0.8
O2 B:VO4259 4.1 21.1 0.8
NE2 B:HIS78 4.2 21.1 1.0
ND1 B:HIS143 4.2 15.7 1.0
CG B:HIS76 4.2 14.2 1.0
CG B:HIS143 4.3 15.9 1.0
ND1 B:HIS76 4.3 14.2 1.0
NE2 B:HIS81 4.3 13.3 1.0
CD2 B:HIS78 4.3 21.6 1.0
CD2 B:HIS81 4.4 15.3 1.0
OD1 B:ASP164 4.4 15.6 1.0
CE1 B:HIS200 4.6 16.6 1.0
OD1 B:ASP80 4.7 16.8 1.0
O4 B:VO4259 4.9 26.7 0.8
NE2 B:HIS200 5.0 17.3 1.0

Reference:

K.Podzelinska, Y.M.Kim, D.Zechel, F.Faucher, Z.Jia. Crystal Structure of Phnp in Complex with Orthovanadate To Be Published.
Page generated: Tue Dec 15 04:13:44 2020

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