Magnesium in PDB 6yso: Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing

Enzymatic activity of Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing

All present enzymatic activity of Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing:
7.2.2.10;

Protein crystallography data

The structure of Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing, PDB code: 6yso was solved by K.El Omari, N.Mohamad, K.Bountra, R.Duman, M.Romano, K.Schlegel, H.Kwong, V.Mykhaylyk, C.E.Olesen, J.V.Moller, M.Bublitz, K.Beis, A.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.59 / 3.13
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 131.140, 94.390, 135.110, 90.00, 107.05, 90.00
R / Rfree (%) 20.1 / 25.9

Other elements in 6yso:

The structure of Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing also contains other interesting chemical elements:

Potassium (K) 2 atoms
Vanadium (V) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing (pdb code 6yso). 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 (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing, PDB code: 6yso:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6yso

Go back to Magnesium Binding Sites List in 6yso
Magnesium binding site 1 out of 4 in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing


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 (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:98.7
occ:1.00
O A:HOH1104 1.9 0.1 1.0
OD2 A:ASP351 2.0 0.7 1.0
O A:HOH1102 2.0 87.2 1.0
O A:THR353 2.0 66.3 1.0
OD1 A:ASP703 2.1 78.0 1.0
O3 A:VN41002 2.3 0.1 1.0
CG A:ASP703 3.1 77.1 1.0
CG A:ASP351 3.2 91.6 1.0
C A:THR353 3.2 82.1 1.0
OD2 A:ASP703 3.6 85.3 1.0
V A:VN41002 3.7 0.0 1.0
OG1 A:THR353 3.7 0.4 1.0
OD1 A:ASP351 3.8 0.0 1.0
N A:GLY354 4.1 80.2 1.0
CA A:GLY354 4.1 73.3 1.0
O A:GLY182 4.2 82.0 1.0
N A:GLY704 4.2 83.2 1.0
CA A:THR353 4.3 85.0 1.0
OD2 A:ASP707 4.3 95.6 1.0
N A:THR353 4.3 85.7 1.0
CB A:ASP351 4.3 70.8 1.0
CB A:ASP703 4.4 73.3 1.0
O1 A:VN41002 4.6 92.0 1.0
OG1 A:THR355 4.6 65.2 1.0
CB A:THR353 4.6 78.3 1.0
C A:GLY354 4.6 64.8 1.0
N A:ASP703 4.6 75.2 1.0
N A:THR355 4.7 65.5 1.0
CA A:GLY704 4.8 97.8 1.0
C A:ASP703 4.8 82.0 1.0
CA A:GLY182 4.9 77.4 1.0
O2 A:VN41002 4.9 0.2 1.0
CA A:ASP703 4.9 77.4 1.0
C A:GLY182 5.0 80.2 1.0
C A:LYS352 5.0 86.5 1.0

Magnesium binding site 2 out of 4 in 6yso

Go back to Magnesium Binding Sites List in 6yso
Magnesium binding site 2 out of 4 in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing


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 (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:0.9
occ:1.00
OD1 A:ASN628 1.9 0.3 1.0
O A:HOH1103 2.0 0.6 1.0
O3G A:1281000 2.0 0.6 1.0
O1B A:1281000 2.9 0.2 1.0
CG A:ASN628 3.1 0.9 1.0
PG A:1281000 3.3 0.1 1.0
ND2 A:ASN628 3.8 0.8 1.0
PB A:1281000 3.9 0.2 1.0
O1G A:1281000 4.0 0.7 1.0
NH2 A:ARG560 4.0 95.4 1.0
O3B A:1281000 4.1 0.8 1.0
N7 A:1281000 4.2 0.8 1.0
CB A:ASN628 4.3 0.3 1.0
O2B A:1281000 4.4 0.8 1.0
O2G A:1281000 4.5 0.3 1.0
C8 A:1281000 4.8 0.7 1.0
N6 A:1281000 5.0 99.5 1.0

Magnesium binding site 3 out of 4 in 6yso

Go back to Magnesium Binding Sites List in 6yso
Magnesium binding site 3 out of 4 in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing


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 (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2003

b:93.2
occ:1.00
O B:HOH2102 2.0 74.6 1.0
OD1 B:ASP703 2.0 88.5 1.0
OD2 B:ASP351 2.0 94.5 1.0
O B:THR353 2.1 96.6 1.0
O B:HOH2104 2.3 0.9 1.0
O3 B:VN42002 2.4 0.7 1.0
CG B:ASP703 2.9 92.6 1.0
OD2 B:ASP703 3.0 62.6 1.0
CG B:ASP351 3.2 79.6 1.0
C B:THR353 3.3 87.4 1.0
V B:VN42002 3.8 99.5 1.0
OD1 B:ASP351 3.9 81.8 1.0
OD2 B:ASP707 4.0 0.8 1.0
O B:GLY182 4.1 76.2 1.0
N B:GLY354 4.2 86.2 1.0
CA B:GLY354 4.2 98.9 1.0
CA B:THR353 4.2 81.2 1.0
CB B:THR353 4.3 74.6 1.0
N B:GLY704 4.3 82.5 1.0
CB B:ASP703 4.3 89.3 1.0
CB B:ASP351 4.3 70.5 1.0
OG1 B:THR355 4.4 0.7 1.0
N B:THR353 4.4 77.6 1.0
CG2 B:THR353 4.5 76.5 1.0
N B:ASP703 4.6 97.7 1.0
N B:THR355 4.6 98.4 1.0
CA B:GLY182 4.7 66.2 1.0
O2 B:VN42002 4.7 0.5 1.0
CA B:GLY704 4.7 84.3 1.0
C B:GLY354 4.8 92.8 1.0
CA B:ASP703 4.9 90.0 1.0
C B:GLY182 4.9 73.2 1.0
O1 B:VN42002 4.9 96.7 1.0
C B:ASP703 4.9 80.0 1.0
CG B:ASP707 5.0 97.9 1.0

Magnesium binding site 4 out of 4 in 6yso

Go back to Magnesium Binding Sites List in 6yso
Magnesium binding site 4 out of 4 in the Crystal Structure of the (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing


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 (Sr) CA2+-Atpase Solved By Vanadium Sad Phasing within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2004

b:0.2
occ:1.00
OD1 B:ASN628 1.9 0.9 1.0
O B:HOH2103 2.2 0.4 1.0
O3G B:1282000 2.2 0.5 1.0
O2B B:1282000 2.6 0.1 1.0
CG B:ASN628 2.9 0.5 1.0
PG B:1282000 3.1 0.7 1.0
ND2 B:ASN628 3.3 0.2 1.0
O1G B:1282000 3.3 0.1 1.0
O3B B:1282000 3.7 0.2 1.0
PB B:1282000 3.7 0.8 1.0
N7 B:1282000 4.2 0.8 1.0
CB B:ASN628 4.3 0.7 1.0
O2G B:1282000 4.6 0.2 1.0
C8 B:1282000 4.6 0.2 1.0
O1B B:1282000 4.7 0.6 1.0
OD1 B:ASP627 4.8 0.1 1.0
NH2 B:ARG560 4.8 0.2 1.0
NH1 B:ARG678 4.9 93.6 1.0
O3A B:1282000 4.9 0.4 1.0

Reference:

K.El Omari, N.Mohamad, K.Bountra, R.Duman, M.Romano, K.Schlegel, H.S.Kwong, V.Mykhaylyk, C.Olesen, J.V.Moller, M.Bublitz, K.Beis, A.Wagner. Experimental Phasing with Vanadium and Application to Nucleotide-Binding Membrane Proteins. Iucrj V. 7 1092 2020.
ISSN: ESSN 2052-2525
PubMed: 33209320
DOI: 10.1107/S2052252520012312
Page generated: Tue Dec 15 02:27:53 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy