Magnesium in PDB 6rj4: Molybdenum Storage Protein - P6422, Adp

Protein crystallography data

The structure of Molybdenum Storage Protein - P6422, Adp, PDB code: 6rj4 was solved by U.Ermler, S.Bruenle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.17 / 1.90
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 188.680, 188.680, 188.630, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 20

Other elements in 6rj4:

The structure of Molybdenum Storage Protein - P6422, Adp also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Molybdenum Storage Protein - P6422, Adp (pdb code 6rj4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Molybdenum Storage Protein - P6422, Adp, PDB code: 6rj4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6rj4

Go back to Magnesium Binding Sites List in 6rj4
Magnesium binding site 1 out of 4 in the Molybdenum Storage Protein - P6422, Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Molybdenum Storage Protein - P6422, Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:27.2
occ:1.00
O1B A:ATP301 2.0 28.6 1.0
O A:PRO227 2.0 34.6 1.0
OE2 A:GLU190 2.0 41.3 1.0
O A:HOH419 2.1 27.6 1.0
O2A A:ATP301 2.1 27.5 1.0
O A:HOH404 2.2 24.9 1.0
CD A:GLU190 3.0 37.6 1.0
C A:PRO227 3.2 32.3 1.0
PB A:ATP301 3.3 32.1 1.0
OE1 A:GLU190 3.3 37.7 1.0
PA A:ATP301 3.3 33.2 1.0
O3A A:ATP301 3.7 38.0 1.0
O B:HOH416 3.9 30.8 1.0
OD2 A:ASP171 3.9 32.1 1.0
NZ A:LYS45 4.0 35.5 1.0
O A:HOH457 4.0 30.9 1.0
CA A:PRO227 4.1 32.3 1.0
O3G A:ATP301 4.1 28.4 1.0
OD1 A:ASP171 4.2 30.4 1.0
N A:VAL228 4.2 32.7 1.0
C5' A:ATP301 4.3 35.2 1.0
O A:HOH458 4.3 31.2 1.0
O5' A:ATP301 4.3 39.6 1.0
O2B A:ATP301 4.4 32.5 1.0
CG A:GLU190 4.4 31.5 1.0
CB A:PRO227 4.4 33.0 1.0
CA A:VAL228 4.4 28.1 1.0
O3B A:ATP301 4.4 29.1 1.0
O1A A:ATP301 4.4 42.4 1.0
CG A:ASP171 4.5 31.7 1.0
PG A:ATP301 4.8 28.2 1.0
CG1 A:VAL228 4.9 26.4 1.0
O A:HOH415 5.0 25.4 1.0

Magnesium binding site 2 out of 4 in 6rj4

Go back to Magnesium Binding Sites List in 6rj4
Magnesium binding site 2 out of 4 in the Molybdenum Storage Protein - P6422, Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Molybdenum Storage Protein - P6422, Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:40.9
occ:1.00
O3B D:ADP301 1.9 33.4 0.7
O1A D:ADP301 2.0 38.7 0.7
O D:HOH433 2.2 40.5 1.0
O D:HOH442 2.2 35.6 1.0
O D:HOH526 2.3 44.7 1.0
O D:HOH408 2.4 35.8 1.0
PA D:ADP301 3.1 37.7 0.7
PB D:ADP301 3.1 26.4 0.7
O3A D:ADP301 3.1 37.1 0.7
O2 D:PO4303 3.7 27.0 1.0
O D:HOH420 3.9 39.5 1.0
O5' D:ADP301 3.9 38.1 0.7
O2B D:ADP301 4.0 30.7 0.7
NZ D:LYS42 4.1 25.2 1.0
O1B D:ADP301 4.1 36.5 0.7
OD2 D:ASP170 4.3 27.4 1.0
O2A D:ADP301 4.4 39.9 0.7
OD1 D:ASP170 4.5 27.5 1.0
O3 D:PO4303 4.6 33.5 1.0
NZ D:LYS189 4.7 45.6 1.0
OE1 D:GLU227 4.7 31.1 1.0
CG D:ASP170 4.7 28.9 1.0
P D:PO4303 4.8 31.2 1.0
CE D:LYS189 4.8 49.9 1.0
O D:HOH514 4.9 49.5 1.0
OE1 D:GLN46 4.9 51.7 0.5

Magnesium binding site 3 out of 4 in 6rj4

Go back to Magnesium Binding Sites List in 6rj4
Magnesium binding site 3 out of 4 in the Molybdenum Storage Protein - P6422, Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Molybdenum Storage Protein - P6422, Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:26.1
occ:1.00
O1B C:ATP301 2.0 23.3 1.0
O C:HOH406 2.0 26.4 1.0
O2A C:ATP301 2.1 28.8 1.0
O C:HOH413 2.1 25.9 1.0
O C:PRO227 2.1 28.8 1.0
OE2 C:GLU190 2.1 31.8 1.0
CD C:GLU190 3.1 32.7 1.0
PB C:ATP301 3.3 25.4 1.0
PA C:ATP301 3.3 30.7 1.0
C C:PRO227 3.3 26.2 1.0
OE1 C:GLU190 3.4 30.8 1.0
O3A C:ATP301 3.6 30.8 1.0
OD2 C:ASP171 3.9 30.2 1.0
O C:HOH466 3.9 26.1 1.0
NZ C:LYS45 4.0 23.5 1.0
O C:HOH474 4.0 27.9 1.0
O3G C:ATP301 4.1 24.2 1.0
CA C:PRO227 4.2 28.9 1.0
OD1 C:ASP171 4.2 26.9 1.0
N C:VAL228 4.2 27.3 1.0
O C:HOH504 4.3 30.9 1.0
O3B C:ATP301 4.3 28.1 1.0
CA C:VAL228 4.4 26.6 1.0
O5' C:ATP301 4.4 34.9 1.0
O2B C:ATP301 4.4 26.4 1.0
O1A C:ATP301 4.4 32.0 1.0
C5' C:ATP301 4.5 30.4 1.0
CG C:ASP171 4.5 27.0 1.0
CG C:GLU190 4.5 30.8 1.0
CB C:PRO227 4.5 32.2 1.0
PG C:ATP301 4.7 25.6 1.0
CG1 C:VAL228 4.9 23.6 1.0
O C:HOH408 4.9 33.5 1.0
O2G C:ATP301 4.9 27.9 1.0

Magnesium binding site 4 out of 4 in 6rj4

Go back to Magnesium Binding Sites List in 6rj4
Magnesium binding site 4 out of 4 in the Molybdenum Storage Protein - P6422, Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Molybdenum Storage Protein - P6422, Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:27.7
occ:1.00
O1B E:ATP301 2.0 30.1 1.0
O E:HOH403 2.0 25.6 1.0
O E:HOH417 2.0 25.5 1.0
O2A E:ATP301 2.1 32.5 1.0
OE2 E:GLU190 2.1 39.1 1.0
O E:PRO227 2.1 37.6 1.0
CD E:GLU190 3.0 38.3 1.0
PB E:ATP301 3.3 29.9 1.0
OE1 E:GLU190 3.3 35.3 1.0
C E:PRO227 3.3 34.4 1.0
PA E:ATP301 3.4 34.2 1.0
O3A E:ATP301 3.6 30.4 1.0
OD2 E:ASP171 3.8 32.8 1.0
NZ E:LYS45 3.9 26.7 1.0
O F:HOH453 3.9 35.7 1.0
O E:HOH466 4.0 29.1 1.0
OD1 E:ASP171 4.1 31.3 1.0
O3G E:ATP301 4.2 27.9 1.0
CA E:PRO227 4.2 34.9 1.0
O E:HOH475 4.2 27.2 1.0
O3B E:ATP301 4.3 30.9 1.0
N E:VAL228 4.3 30.9 1.0
O2B E:ATP301 4.4 27.1 1.0
CA E:VAL228 4.4 27.4 1.0
O1A E:ATP301 4.4 34.9 1.0
CG E:ASP171 4.4 29.7 1.0
O5' E:ATP301 4.4 34.8 1.0
CG E:GLU190 4.4 34.2 1.0
C5' E:ATP301 4.5 31.9 1.0
CB E:PRO227 4.5 31.9 1.0
PG E:ATP301 4.7 29.7 1.0
CG1 E:VAL228 4.9 35.0 1.0
O2G E:ATP301 4.9 27.0 1.0
O E:HOH419 5.0 32.4 1.0

Reference:

S.Brunle, M.L.Eisinger, J.Poppe, D.J.Mills, J.D.Langer, J.Vonck, U.Ermler. Molybdate Pumping Into the Molybdenum Storage Protein Via An Atp-Powered Piercing Mechanism. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31811022
DOI: 10.1073/PNAS.1913031116
Page generated: Mon Dec 14 23:59:41 2020

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