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Magnesium in PDB 2aer: Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.

Enzymatic activity of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.

All present enzymatic activity of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex., PDB code: 2aer was solved by S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, M.S.Bajaj, A.Liesum, J.Dumas, D.Prevost, H.Schreuder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.900, 81.200, 125.900, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 25.6

Other elements in 2aer:

The structure of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. 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 Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. (pdb code 2aer). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex., PDB code: 2aer:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2aer

Go back to Magnesium Binding Sites List in 2aer
Magnesium binding site 1 out of 3 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


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 Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg3001

b:33.5
occ:1.00
OE11 L:CGU25 1.9 33.2 1.0
OE21 L:CGU29 2.0 30.2 1.0
OE21 L:CGU25 2.0 27.5 1.0
O L:HOH3147 2.1 30.8 1.0
O L:HOH3097 2.1 21.1 1.0
OE11 L:CGU29 2.3 30.6 1.0
CD1 L:CGU25 2.8 31.4 1.0
CD2 L:CGU25 2.8 28.8 1.0
CD2 L:CGU29 2.9 30.4 1.0
CG L:CGU25 3.0 30.0 1.0
CD1 L:CGU29 3.1 30.0 1.0
CG L:CGU29 3.3 29.2 1.0
OE22 L:CGU25 3.9 29.1 1.0
NH1 L:ARG28 4.0 33.9 1.0
OE12 L:CGU25 4.0 33.7 1.0
O L:HOH3052 4.0 20.8 1.0
OE22 L:CGU29 4.1 31.0 1.0
OE12 L:CGU29 4.3 30.8 1.0
CB L:CGU25 4.5 28.8 1.0
CA L:CA3002 4.6 67.8 1.0
O L:CGU25 4.7 26.5 1.0
CB L:CGU29 4.8 29.2 1.0

Magnesium binding site 2 out of 3 in 2aer

Go back to Magnesium Binding Sites List in 2aer
Magnesium binding site 2 out of 3 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


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 Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg3004

b:37.1
occ:1.00
OE11 L:CGU26 1.9 31.6 1.0
OE21 L:CGU16 1.9 39.4 1.0
OE11 L:CGU16 1.9 37.2 1.0
OE22 L:CGU26 2.1 35.1 1.0
O L:HOH3131 2.1 33.8 1.0
CD1 L:CGU16 2.8 36.8 1.0
CD2 L:CGU16 2.9 37.7 1.0
CD1 L:CGU26 2.9 32.4 1.0
CD2 L:CGU26 3.0 33.7 1.0
CG L:CGU16 3.3 37.5 1.0
CG L:CGU26 3.4 32.4 1.0
O L:HOH3086 3.4 23.0 1.0
CA L:CA3005 3.6 60.5 1.0
CB L:CGU16 3.9 38.1 1.0
OE12 L:CGU16 3.9 36.6 1.0
OE22 L:CGU16 4.0 36.8 1.0
OE12 L:CGU26 4.0 32.9 1.0
CB L:CGU26 4.0 29.2 1.0
OD1 L:ASN2 4.2 65.1 1.0
OE21 L:CGU26 4.2 36.8 1.0
OE12 L:CGU7 4.3 33.5 1.0
OE11 L:CGU7 4.4 35.2 1.0
O L:HOH3153 4.5 49.6 1.0
O L:HOH3124 4.5 48.6 1.0
O L:ALA1 4.6 64.9 1.0
CD1 L:CGU7 4.8 33.7 1.0
CA L:CA3003 4.9 69.1 1.0
CA L:CGU16 5.0 39.5 1.0

Magnesium binding site 3 out of 3 in 2aer

Go back to Magnesium Binding Sites List in 2aer
Magnesium binding site 3 out of 3 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


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 Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg3007

b:51.4
occ:1.00
OE12 L:CGU14 1.9 54.5 1.0
CD1 L:CGU14 1.9 52.4 1.0
OE12 L:CGU19 2.0 60.1 1.0
OE11 L:CGU14 2.0 54.2 1.0
OE22 L:CGU14 2.2 52.6 1.0
CD1 L:CGU19 2.4 59.4 1.0
OE11 L:CGU19 2.6 59.7 1.0
CD2 L:CGU14 2.9 51.8 1.0
CG L:CGU14 2.9 50.8 1.0
OE21 L:CGU19 3.3 60.6 1.0
CG L:CGU19 3.6 59.1 1.0
CB L:CGU14 3.9 46.6 1.0
CD2 L:CGU19 3.9 60.5 1.0
OE21 L:CGU14 4.1 53.0 1.0
O L:CGU14 4.2 42.0 1.0
CB L:CGU19 4.2 56.3 1.0
C L:CGU14 4.3 42.5 1.0
CA L:CGU14 4.6 43.2 1.0
N L:ARG15 4.8 42.3 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: Mon Dec 14 07:15:00 2020

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