Atomistry » Manganese » PDB 5nha-5raa » 5olk
Atomistry »
  Manganese »
    PDB 5nha-5raa »
      5olk »

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

Go back to Manganese Binding Sites List in 5olk
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

Go back to Manganese Binding Sites List in 5olk
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

Go back to Manganese Binding Sites List in 5olk
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

Go back to Manganese Binding Sites List in 5olk
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

Go back to Manganese Binding Sites List in 5olk
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

Go back to Manganese Binding Sites List in 5olk
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

Go back to Manganese Binding Sites List in 5olk
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

Go back to Manganese Binding Sites List in 5olk
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: Sun Oct 6 02:20:51 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy