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Magnesium 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:

Manganese (Mn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis, PDB code: 5olk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5olk

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1003

b:48.3
occ:1.00
 O1G A:DTP1002 1.9 83.3 1.0
O1A A:DTP1002 2.1 61.2 1.0
O2B A:DTP1002 2.3 57.9 1.0
O2A A:DTP1001 2.3 50.9 1.0
O2B A:DTP1001 2.3 54.9 1.0
O1G A:DTP1001 2.4 88.1 1.0
PB A:DTP1002 3.2 60.8 1.0
PG A:DTP1002 3.2 84.3 1.0
PA A:DTP1002 3.4 59.3 1.0
O3B A:DTP1002 3.5 75.0 1.0
O3A A:DTP1002 3.5 59.1 1.0
PB A:DTP1001 3.6 59.8 1.0
PA A:DTP1001 3.6 52.4 1.0
PG A:DTP1001 3.7 86.2 1.0
O3A A:DTP1001 3.8 58.4 1.0
O3B A:DTP1001 4.0 73.5 1.0
O2G A:DTP1002 4.2 85.0 1.0
NH1 A:ARG12 4.2 38.4 1.0
C5' A:DTP1002 4.2 56.6 1.0
O5' A:DTP1002 4.2 59.9 1.0
C5' A:DTP1001 4.3 54.5 1.0
O3G A:DTP1002 4.3 84.5 1.0
O5' A:DTP1001 4.3 55.6 1.0
NH2 A:ARG12 4.4 39.3 1.0
O2A A:DTP1002 4.5 59.4 1.0
O2G A:DTP1001 4.5 87.7 1.0
O1B A:DTP1002 4.6 58.0 1.0
O1A A:DTP1001 4.7 51.5 1.0
O3G A:DTP1001 4.8 86.0 1.0
O1B A:DTP1001 4.8 58.2 1.0
CZ A:ARG12 4.8 56.6 1.0

Magnesium binding site 2 out of 4 in 5olk

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg1003

b:62.6
occ:1.00
 O2G B:DTP1001 2.2 0.5 1.0
O2A B:DTP1002 2.3 66.1 1.0
O2G B:DTP1002 2.3 81.1 1.0
O1A B:DTP1001 2.4 83.9 1.0
O1B B:DTP1001 2.5 87.8 1.0
O1B B:DTP1002 2.9 72.2 1.0
PG B:DTP1002 3.4 83.5 1.0
PB B:DTP1002 3.5 71.1 1.0
PG B:DTP1001 3.6 1.0 1.0
PA B:DTP1002 3.6 67.1 1.0
PB B:DTP1001 3.6 89.8 1.0
O1G B:DTP1002 3.6 85.2 1.0
O3A B:DTP1002 3.7 70.6 1.0
PA B:DTP1001 3.7 84.7 1.0
O3B B:DTP1002 3.8 76.9 1.0
O3A B:DTP1001 3.9 88.1 1.0
O3B B:DTP1001 3.9 99.3 1.0
NH1 B:ARG12 4.4 75.6 1.0
O1G B:DTP1001 4.5 0.1 1.0
O5' B:DTP1002 4.5 65.7 1.0
C5' B:DTP1002 4.6 67.0 1.0
O3G B:DTP1001 4.6 0.7 1.0
O5' B:DTP1001 4.6 82.9 1.0
O1A B:DTP1002 4.6 66.6 1.0
C5' B:DTP1001 4.6 81.5 1.0
O2A B:DTP1001 4.7 87.7 1.0
NH2 B:ARG12 4.8 58.5 1.0
O3G B:DTP1002 4.9 81.5 1.0
O2B B:DTP1001 4.9 83.6 1.0

Magnesium binding site 3 out of 4 in 5olk

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Atp-Cone-Containing Nrdb From Leeuwenhoekiella Blandensis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg1003

b:28.4
occ:1.00
 O1A C:DTP1001 2.1 42.8 1.0
O1A C:DTP1002 2.2 49.5 1.0
O3G C:DTP1002 2.2 61.8 1.0
O2B C:DTP1001 2.3 49.9 1.0
O2G C:DTP1001 2.4 78.3 1.0
O2B C:DTP1002 2.5 44.1 1.0
PA C:DTP1001 3.4 46.5 1.0
PB C:DTP1001 3.4 52.6 1.0
PB C:DTP1002 3.5 47.5 1.0
PA C:DTP1002 3.5 49.7 1.0
PG C:DTP1002 3.6 62.5 1.0
O3A C:DTP1001 3.7 50.2 1.0
PG C:DTP1001 3.7 81.5 1.0
O3A C:DTP1002 3.8 49.8 1.0
O3B C:DTP1001 3.8 66.0 1.0
O3B C:DTP1002 3.9 53.2 1.0
C5' C:DTP1001 4.2 50.5 1.0
O5' C:DTP1001 4.2 48.9 1.0
C5' C:DTP1002 4.2 53.5 1.0
NH1 C:ARG12 4.2 40.7 1.0
O5' C:DTP1002 4.2 54.5 1.0
O2G C:DTP1002 4.4 61.2 1.0
O2A C:DTP1001 4.5 43.9 1.0
O2A C:DTP1002 4.6 51.4 1.0
NH2 C:ARG12 4.6 36.5 1.0
O1G C:DTP1002 4.7 65.1 1.0
O3G C:DTP1001 4.7 81.7 1.0
O1B C:DTP1001 4.7 54.8 1.0
O1G C:DTP1001 4.7 85.3 1.0
O1B C:DTP1002 4.9 42.7 1.0
CZ C:ARG12 4.9 46.6 1.0

Magnesium binding site 4 out of 4 in 5olk

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg1003

b:52.4
occ:1.00
 O2A D:DTP1002 2.1 64.8 1.0
O2A D:DTP1001 2.3 85.0 1.0
O2B D:DTP1001 2.3 92.0 1.0
O2G D:DTP1001 2.3 0.9 1.0
O1B D:DTP1002 2.4 69.2 1.0
O3G D:DTP1002 2.4 96.8 1.0
PG D:DTP1002 3.4 95.9 1.0
PB D:DTP1002 3.4 66.9 1.0
PA D:DTP1002 3.4 64.5 1.0
PB D:DTP1001 3.5 93.2 1.0
O1G D:DTP1002 3.6 94.5 1.0
PA D:DTP1001 3.6 84.9 1.0
O3A D:DTP1002 3.6 61.6 1.0
PG D:DTP1001 3.7 0.4 1.0
O3B D:DTP1002 3.7 84.3 1.0
O3A D:DTP1001 3.8 90.3 1.0
O3B D:DTP1001 3.9 0.7 1.0
NH1 D:ARG12 4.2 75.9 1.0
O5' D:DTP1002 4.3 64.0 1.0
C5' D:DTP1002 4.3 62.9 1.0
C5' D:DTP1001 4.3 83.5 1.0
O5' D:DTP1001 4.4 84.5 1.0
O1A D:DTP1002 4.5 63.3 1.0
NH2 D:ARG12 4.6 65.2 1.0
O3G D:DTP1001 4.6 0.1 1.0
O1A D:DTP1001 4.7 83.7 1.0
O1G D:DTP1001 4.7 0.9 1.0
O1B D:DTP1001 4.8 92.5 1.0
O2B D:DTP1002 4.8 63.9 1.0
O2G D:DTP1002 4.8 97.5 1.0
CZ D:ARG12 4.9 83.8 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: Mon Sep 30 01:02:13 2024

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