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Magnesium in PDB 2a2q: Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+

Enzymatic activity of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+

All present enzymatic activity of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+:
3.4.21.21;

Protein crystallography data

The structure of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+, PDB code: 2a2q was solved by S.P.Bajaj, M.Bajaj, A.E.Schmidt, K.Padmanabhan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.720, 81.000, 126.120, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.9

Other elements in 2a2q:

The structure of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+ also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 6 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+ (pdb code 2a2q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+, PDB code: 2a2q:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2a2q

Go back to Magnesium Binding Sites List in 2a2q
Magnesium binding site 1 out of 3 in the Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1001

b:26.1
occ:1.00
 OE12 L:CGU25 1.8 30.9 1.0
OE21 L:CGU25 1.9 26.8 1.0
O L:HOH1060 2.1 28.8 1.0
OE21 L:CGU29 2.1 23.7 1.0
O L:HOH1154 2.2 45.6 1.0
OE11 L:CGU29 2.3 25.2 1.0
CD2 L:CGU25 2.6 27.2 1.0
CD1 L:CGU25 2.6 29.8 1.0
CG L:CGU25 2.8 28.0 1.0
CD2 L:CGU29 2.9 23.7 1.0
CD1 L:CGU29 3.0 24.3 1.0
CG L:CGU29 3.0 23.9 1.0
NH1 L:ARG28 3.6 35.9 1.0
OE22 L:CGU25 3.7 27.9 1.0
O L:HOH1054 3.8 27.5 1.0
OE11 L:CGU25 3.8 30.9 1.0
OE22 L:CGU29 4.1 23.2 1.0
O L:HOH1177 4.1 36.0 1.0
OE12 L:CGU29 4.2 25.2 1.0
O L:HOH1110 4.3 27.0 1.0
CB L:CGU25 4.3 26.4 1.0
O L:CGU25 4.4 23.1 1.0
CZ L:ARG28 4.5 35.3 1.0
CB L:CGU29 4.6 23.7 1.0
C L:CGU25 4.9 23.8 1.0
CA L:CA1002 4.9 55.5 1.0

Magnesium binding site 2 out of 3 in 2a2q

Go back to Magnesium Binding Sites List in 2a2q
Magnesium binding site 2 out of 3 in the Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1004

b:19.8
occ:1.00
 OE11 L:CGU16 1.9 23.9 1.0
OE22 L:CGU26 2.0 26.6 1.0
OE21 L:CGU16 2.0 20.4 1.0
OE11 L:CGU26 2.0 27.0 1.0
O L:HOH1053 2.0 31.8 1.0
O L:HOH1095 2.1 21.2 1.0
CD1 L:CGU16 2.8 23.5 1.0
CD1 L:CGU26 2.9 27.8 1.0
CD2 L:CGU16 2.9 22.1 1.0
CD2 L:CGU26 3.0 27.1 1.0
CG L:CGU16 3.3 23.2 1.0
CG L:CGU26 3.4 26.8 1.0
O L:HOH1079 3.8 25.0 1.0
CB L:CGU16 3.9 24.1 1.0
OE12 L:CGU26 3.9 29.8 1.0
OE12 L:CGU16 3.9 24.7 1.0
CA L:CA1005 4.0 51.9 1.0
OE22 L:CGU16 4.0 21.4 1.0
CA L:CA1003 4.0 53.5 1.0
OE21 L:CGU26 4.1 29.2 1.0
CB L:CGU26 4.1 24.9 1.0
OE11 L:CGU7 4.3 31.1 1.0
OE12 L:CGU7 4.3 29.9 1.0
O L:HOH1149 4.5 35.9 1.0
OD1 L:ASN2 4.5 52.6 1.0
O L:ALA1 4.6 52.8 1.0
O L:HOH1073 4.7 47.3 1.0
O L:HOH1157 4.7 39.9 1.0
CD1 L:CGU7 4.8 29.9 1.0
CA L:CGU16 5.0 26.1 1.0

Magnesium binding site 3 out of 3 in 2a2q

Go back to Magnesium Binding Sites List in 2a2q
Magnesium binding site 3 out of 3 in the Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex of Active-Site Inhibited Human Coagulation Factor Viia with Human Soluble Tissue Factor in the Presence of CA2+, MG2+, Na+, and ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1007

b:41.1
occ:1.00
 OE12 L:CGU19 1.9 44.0 1.0
OE22 L:CGU19 1.9 41.5 1.0
OE22 L:CGU14 1.9 36.6 1.0
OE11 L:CGU14 2.0 35.5 1.0
CD1 L:CGU14 2.6 34.6 1.0
CD2 L:CGU14 2.6 36.1 1.0
CG L:CGU14 2.6 34.3 1.0
CD1 L:CGU19 2.7 42.4 1.0
CD2 L:CGU19 2.7 41.3 1.0
CG L:CGU19 3.2 41.5 1.0
OE11 L:CGU19 3.7 44.2 1.0
OE12 L:CGU14 3.8 35.5 1.0
OE21 L:CGU19 3.8 41.5 1.0
OE21 L:CGU14 3.9 36.9 1.0
CB L:CGU19 4.1 39.0 1.0
CB L:CGU14 4.2 31.3 1.0
O L:CGU14 4.2 27.8 1.0
C L:CGU14 4.5 28.6 1.0
CA L:CGU14 4.8 29.4 1.0
CA L:CGU19 4.9 37.5 1.0
N L:CGU19 4.9 36.0 1.0

Reference:

S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, K.Padmanabhan. High Resolution Structures of P-Aminobenzamidine- and Benzamidine-Viia/Soluble Tissue Factor: Unpredicted Conformation of the 192-193 Peptide Bond and Mapping of CA2+, MG2+, Na+, and ZN2+ Sites in Factor Viia. J.Biol.Chem. V. 281 24873 2006.
ISSN: ISSN 0021-9258
PubMed: 16757484
DOI: 10.1074/JBC.M509971200
Page generated: Tue Aug 13 20:20:47 2024

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