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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: Wed Oct 2 01:06:03 2024

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