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Manganese in PDB 5olk: Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis

Enzymatic activity of Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis

All present enzymatic activity of Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis, PDB code: 5olk was solved by M.Hasan, A.R.Grinberg, B.M.Sjoberg, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.70 / 2.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 74.003, 90.542, 90.948, 110.78, 98.99, 114.11
R / Rfree (%) 20.5 / 23.8

Other elements in 5olk:

The structure of Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis (pdb code 5olk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis, PDB code: 5olk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5olk

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Manganese binding site 1 out of 8 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


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 the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1004

b:71.8
occ:1.00
 OE2 A:GLU263 2.2 72.1 1.0
OE1 A:GLU298 2.4 66.1 1.0
OE2 A:GLU200 2.5 48.8 1.0
OE1 A:GLU263 2.6 65.9 1.0
CD A:GLU263 2.7 73.4 1.0
ND1 A:HIS301 2.7 51.5 1.0
OE2 A:GLU298 2.9 45.1 1.0
O A:HOH1121 2.9 45.9 1.0
O A:HOH1126 3.0 67.8 1.0
CD A:GLU298 3.0 65.1 1.0
CD A:GLU200 3.6 49.0 1.0
CE1 A:HIS301 3.6 50.9 1.0
MN A:MN1005 3.7 54.5 1.0
CG A:HIS301 3.8 49.3 1.0
O A:HOH1106 4.1 65.8 1.0
CB A:HIS301 4.1 46.0 1.0
CG A:GLU263 4.1 54.7 1.0
OE1 A:GLU200 4.3 44.7 1.0
NE1 A:TRP177 4.3 49.3 1.0
CG A:GLU200 4.5 41.6 1.0
CG A:GLU298 4.5 51.2 1.0
CD1 A:TRP177 4.7 50.5 1.0
NE2 A:HIS301 4.8 51.5 1.0
CB A:GLU263 4.8 53.1 1.0
CD2 A:HIS301 4.9 51.7 1.0
CZ A:PHE258 5.0 51.2 1.0

Manganese binding site 2 out of 8 in 5olk

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Manganese binding site 2 out of 8 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


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 the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1005

b:54.5
occ:1.00
 OE1 A:GLU200 2.3 44.7 1.0
OE2 A:GLU298 2.3 45.1 1.0
OE1 A:GLU170 2.4 43.9 1.0
ND1 A:HIS203 2.5 50.5 1.0
OE2 A:GLU200 2.6 48.8 1.0
OE2 A:GLU170 2.6 46.0 1.0
CD A:GLU200 2.8 49.0 1.0
CD A:GLU170 2.9 54.7 1.0
O A:HOH1126 3.0 67.8 1.0
CG A:HIS203 3.5 48.7 1.0
CD A:GLU298 3.5 65.1 1.0
CE1 A:HIS203 3.5 49.3 1.0
CB A:HIS203 3.6 45.5 1.0
MN A:MN1004 3.7 71.8 1.0
OE1 A:GLU298 4.2 66.1 1.0
NZ A:LYS174 4.3 45.9 1.0
CG A:GLU200 4.3 41.6 1.0
CG A:GLU170 4.4 48.5 1.0
CG A:GLU298 4.5 51.2 1.0
CG2 A:THR294 4.6 44.6 1.0
CD2 A:HIS203 4.6 50.1 1.0
NE2 A:HIS203 4.7 49.8 1.0
CD A:LYS174 4.9 61.3 1.0
CA A:GLU200 5.0 41.0 1.0
O A:HOH1106 5.0 65.8 1.0
O A:HOH1121 5.0 45.9 1.0

Manganese binding site 3 out of 8 in 5olk

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Manganese binding site 3 out of 8 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


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 the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1004

b:63.9
occ:1.00
 OE1 B:GLU170 2.3 56.4 1.0
OE2 B:GLU298 2.4 62.1 1.0
OE1 B:GLU200 2.4 51.6 1.0
OE2 B:GLU170 2.6 44.6 1.0
ND1 B:HIS203 2.6 49.7 1.0
OE2 B:GLU200 2.7 49.3 1.0
CD B:GLU170 2.8 64.0 1.0
CD B:GLU200 2.9 42.0 1.0
O B:HOH1118 3.3 66.9 1.0
CD B:GLU298 3.5 67.0 1.0
MN B:MN1005 3.6 67.0 1.0
CG B:HIS203 3.6 47.5 1.0
CE1 B:HIS203 3.7 48.2 1.0
CB B:HIS203 3.7 44.5 1.0
NZ B:LYS174 4.1 51.8 1.0
OE1 B:GLU298 4.2 63.2 1.0
CG B:GLU170 4.3 56.2 1.0
CG B:GLU200 4.4 38.6 1.0
CG B:GLU298 4.5 45.9 1.0
O B:HOH1115 4.6 46.7 1.0
CG2 B:THR294 4.6 40.9 1.0
CD B:LYS174 4.8 53.8 1.0
CD2 B:HIS203 4.8 48.4 1.0
NE2 B:HIS203 4.8 48.2 1.0
CA B:GLU200 5.0 37.5 1.0

Manganese binding site 4 out of 8 in 5olk

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Manganese binding site 4 out of 8 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


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 the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1005

b:67.0
occ:1.00
 OE1 B:GLU263 2.3 56.4 1.0
OE1 B:GLU298 2.3 63.2 1.0
ND1 B:HIS301 2.5 48.0 1.0
OE2 B:GLU200 2.6 49.3 1.0
OE2 B:GLU298 2.7 62.1 1.0
CD B:GLU298 2.8 67.0 1.0
O B:HOH1115 2.9 46.7 1.0
CD B:GLU263 3.0 84.2 1.0
OE2 B:GLU263 3.1 0.3 1.0
CE1 B:HIS301 3.4 47.6 1.0
O B:HOH1118 3.4 66.9 1.0
CD B:GLU200 3.4 42.0 1.0
MN B:MN1004 3.6 63.9 1.0
CG B:HIS301 3.6 46.5 1.0
CB B:HIS301 4.0 44.0 1.0
OE1 B:GLU200 4.0 51.6 1.0
CG B:GLU298 4.3 45.9 1.0
CG B:GLU263 4.3 58.9 1.0
CG B:GLU200 4.4 38.6 1.0
NE1 B:TRP177 4.5 52.5 1.0
NE2 B:HIS301 4.6 48.2 1.0
CD2 B:HIS301 4.7 48.5 1.0
CD1 B:TRP177 4.8 53.0 1.0
CA B:GLU298 4.8 41.7 1.0
ND1 B:HIS203 5.0 49.7 1.0
CB B:GLU263 5.0 51.2 1.0

Manganese binding site 5 out of 8 in 5olk

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Manganese binding site 5 out of 8 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1004

b:69.5
occ:1.00
 OE1 C:GLU170 2.3 82.6 1.0
OE1 C:GLU200 2.3 40.5 1.0
OE1 C:GLU298 2.5 76.5 1.0
OE2 C:GLU170 2.6 88.7 1.0
ND1 C:HIS203 2.7 54.8 1.0
CD C:GLU170 2.8 91.1 1.0
O C:HOH1128 2.8 54.5 1.0
CD C:GLU200 3.1 63.0 1.0
OE2 C:GLU200 3.2 63.3 1.0
MN C:MN1005 3.4 76.8 1.0
CD C:GLU298 3.5 78.8 1.0
CG C:HIS203 3.7 53.0 1.0
CE1 C:HIS203 3.7 53.8 1.0
CB C:HIS203 3.8 50.0 1.0
OE2 C:GLU298 4.1 69.3 1.0
NZ C:LYS174 4.1 64.6 1.0
CG C:GLU170 4.3 71.8 1.0
CG C:GLU298 4.5 66.2 1.0
CG C:GLU200 4.6 52.1 1.0
CD C:LYS174 4.7 51.9 1.0
CG2 C:THR294 4.7 50.8 1.0
CD2 C:HIS203 4.8 54.6 1.0
NE2 C:HIS203 4.9 54.0 1.0
O C:HOH1116 4.9 51.9 1.0
O C:HOH1115 5.0 61.6 1.0
CD1 C:LEU267 5.0 66.2 1.0

Manganese binding site 6 out of 8 in 5olk

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Manganese binding site 6 out of 8 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1005

b:76.8
occ:1.00
 OE2 C:GLU200 2.3 63.3 1.0
OE2 C:GLU298 2.5 69.3 1.0
OE1 C:GLU263 2.7 68.3 1.0
OE1 C:GLU298 2.7 76.5 1.0
ND1 C:HIS301 2.7 54.9 1.0
O C:HOH1115 2.8 61.6 1.0
OE2 C:GLU263 2.8 74.6 1.0
O C:HOH1128 2.9 54.5 1.0
CD C:GLU298 2.9 78.8 1.0
CD C:GLU263 3.1 77.2 1.0
CD C:GLU200 3.4 63.0 1.0
MN C:MN1004 3.4 69.5 1.0
CE1 C:HIS301 3.6 54.2 1.0
OE1 C:GLU200 3.8 40.5 1.0
CG C:HIS301 3.9 53.4 1.0
O C:HOH1116 4.1 51.9 1.0
CB C:HIS301 4.2 49.8 1.0
CG C:GLU298 4.4 66.2 1.0
NE1 C:TRP177 4.5 50.4 1.0
CG C:GLU263 4.5 69.3 1.0
CG C:GLU200 4.6 52.1 1.0
NE2 C:HIS301 4.8 54.8 1.0
CD1 C:TRP177 4.8 51.4 1.0
CD2 C:HIS301 5.0 55.2 1.0
ND1 C:HIS203 5.0 54.8 1.0

Manganese binding site 7 out of 8 in 5olk

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Manganese binding site 7 out of 8 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1004

b:66.0
occ:1.00
 OE2 D:GLU298 2.3 59.5 1.0
OE1 D:GLU200 2.3 60.6 1.0
OE1 D:GLU170 2.4 48.4 1.0
ND1 D:HIS203 2.5 46.0 1.0
OE2 D:GLU170 2.5 60.8 1.0
OE2 D:GLU200 2.7 60.7 1.0
CD D:GLU170 2.8 59.6 1.0
CD D:GLU200 2.9 62.0 1.0
O D:HOH1130 3.1 59.4 1.0
CD D:GLU298 3.4 70.7 1.0
CG D:HIS203 3.5 44.1 1.0
CE1 D:HIS203 3.5 45.8 1.0
CB D:HIS203 3.7 41.0 1.0
MN D:MN1005 3.7 71.1 1.0
OE1 D:GLU298 4.1 86.8 1.0
NZ D:LYS174 4.3 51.0 1.0
CG D:GLU170 4.3 48.1 1.0
CG D:GLU200 4.4 42.7 1.0
CG D:GLU298 4.4 60.4 1.0
CG2 D:THR294 4.6 37.7 1.0
NE2 D:HIS203 4.6 46.2 1.0
CD2 D:HIS203 4.6 46.6 1.0
O D:HOH1127 4.7 48.7 1.0
CD1 D:LEU267 5.0 53.0 1.0
CD D:LYS174 5.0 42.7 1.0

Manganese binding site 8 out of 8 in 5olk

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Manganese binding site 8 out of 8 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1005

b:71.1
occ:1.00
 OE1 D:GLU263 2.2 70.6 1.0
OE1 D:GLU298 2.4 86.8 1.0
OE2 D:GLU200 2.4 60.7 1.0
ND1 D:HIS301 2.7 52.5 1.0
O D:HOH1127 2.7 48.7 1.0
CD D:GLU263 2.9 82.2 1.0
OE2 D:GLU263 2.9 72.3 1.0
OE2 D:GLU298 2.9 59.5 1.0
CD D:GLU298 3.0 70.7 1.0
O D:HOH1130 3.0 59.4 1.0
CD D:GLU200 3.5 62.0 1.0
CE1 D:HIS301 3.5 51.2 1.0
CG D:HIS301 3.7 50.9 1.0
MN D:MN1004 3.7 66.0 1.0
CB D:HIS301 4.0 48.4 1.0
OE1 D:GLU200 4.2 60.6 1.0
CG D:GLU263 4.3 66.3 1.0
NE1 D:TRP177 4.3 52.3 1.0
CG D:GLU200 4.4 42.7 1.0
CG D:GLU298 4.5 60.4 1.0
CD1 D:TRP177 4.7 52.5 1.0
NE2 D:HIS301 4.7 51.7 1.0
CD2 D:HIS301 4.8 52.0 1.0
CB D:GLU263 4.9 55.9 1.0
CA D:GLU298 5.0 47.7 1.0

Reference:

I.Rozman Grinberg, D.Lundin, M.Hasan, M.Crona, V.R.Jonna, C.Loderer, M.Sahlin, N.Markova, I.Borovok, G.Berggren, A.Hofer, D.T.Logan, B.M.Sjoberg. Novel Atp-Cone-Driven Allosteric Regulation of Ribonucleotide Reductase Via the Radical-Generating Subunit. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29388911
DOI: 10.7554/ELIFE.31529
Page generated: Tue Dec 15 04:45:35 2020

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