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Calcium in PDB 8cn9: Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII

Enzymatic activity of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII

All present enzymatic activity of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII:
3.4.21.21;

Protein crystallography data

The structure of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII, PDB code: 8cn9 was solved by G.Schluckebier, E.Johansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.50 / 3.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 144.782, 100.794, 181.739, 90, 101.22, 90
R / Rfree (%) 30.3 / 35.6

Other elements in 8cn9:

The structure of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII also contains other interesting chemical elements:

Caesium (Cs) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII (pdb code 8cn9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII, PDB code: 8cn9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 8cn9

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Calcium binding site 1 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:36.7
occ:1.00
 O A:ALA112 2.8 85.8 1.0
CB A:ASN138 3.2 93.2 1.0
O A:ASN138 3.4 92.2 1.0
N A:SER114 3.7 78.9 1.0
C A:PRO113 3.7 76.4 1.0
CA A:PRO113 3.8 72.5 1.0
C A:ALA112 3.8 91.2 1.0
C A:ASN138 3.9 90.4 1.0
CA A:ASN138 4.0 87.1 1.0
OG A:SER114 4.1 65.6 1.0
CB A:SER114 4.2 65.7 1.0
N A:PRO113 4.3 85.3 1.0
O A:PRO113 4.3 89.0 1.0
CG A:ASN138 4.4 86.2 1.0
ND2 A:ASN138 4.4 89.6 1.0
N A:ASN138 4.5 86.4 1.0
CA A:SER114 4.5 73.0 1.0

Calcium binding site 2 out of 10 in 8cn9

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Calcium binding site 2 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:66.5
occ:1.00
 OE1 C:GLU210 2.3 59.5 1.0
OE2 C:GLU220 2.4 48.4 1.0
O C:GLU215 2.7 67.1 1.0
OD1 C:ASP217 2.8 72.3 1.0
O C:ASP212 2.8 55.5 1.0
N C:ASP212 3.3 58.4 1.0
CD C:GLU210 3.4 58.5 1.0
CD C:GLU220 3.5 55.6 1.0
CG C:ASP217 3.5 61.3 1.0
C C:ASP212 3.6 47.2 1.0
CG C:GLU215 3.7 80.4 1.0
OD2 C:ASP217 3.7 56.2 1.0
C C:GLU215 3.7 71.0 1.0
CA C:ASP212 3.8 53.1 1.0
N C:HIS211 3.8 60.0 1.0
OE2 C:GLU210 3.9 40.3 1.0
CB C:ASP212 3.9 56.1 1.0
CG C:GLU220 4.2 55.0 1.0
N C:ASP217 4.2 64.2 1.0
C C:HIS211 4.3 57.5 1.0
OE1 C:GLU220 4.4 68.1 1.0
CA C:HIS211 4.5 51.2 1.0
N C:HIS216 4.5 73.4 1.0
OE2 C:GLU215 4.5 99.1 1.0
CA C:HIS216 4.6 66.3 1.0
NZ C:LYS161 4.6 64.7 1.0
CD C:GLU215 4.6 93.7 1.0
CG C:GLU210 4.6 57.8 1.0
CA C:GLU210 4.7 47.2 1.0
CA C:GLU215 4.7 77.3 1.0
C C:GLU210 4.8 55.8 1.0
CB C:ASP217 4.8 52.4 1.0
CB C:GLU215 4.8 80.8 1.0
CB C:HIS211 4.8 57.5 1.0
N C:GLU215 4.8 68.5 1.0
N C:LEU213 4.9 44.6 1.0
C C:HIS216 4.9 64.7 1.0

Calcium binding site 3 out of 10 in 8cn9

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Calcium binding site 3 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:54.8
occ:1.00
 CA F:ALA112 3.5 54.1 1.0
CB F:PHE139 3.6 53.5 1.0
CB F:ALA112 3.7 69.2 1.0
C F:ALA112 3.8 89.0 1.0
CG2 F:VAL115 3.9 77.1 1.0
N F:PRO113 4.1 76.8 1.0
CD F:PRO113 4.1 73.6 1.0
O F:SER114 4.2 58.8 1.0
N F:SER114 4.4 61.0 1.0
O F:ALA112 4.5 113.0 1.0
CG F:PHE139 4.5 52.4 1.0
O F:ALA111 4.6 55.6 1.0
O F:ASN137 4.6 58.4 1.0
CA F:PHE139 4.6 54.3 1.0
CD1 F:LEU201 4.6 71.5 1.0
C F:SER114 4.6 54.4 1.0
N F:ALA112 4.7 51.8 1.0
CG F:LEU201 4.9 73.2 1.0
CD1 F:PHE139 5.0 55.0 1.0

Calcium binding site 4 out of 10 in 8cn9

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Calcium binding site 4 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca501

b:71.1
occ:1.00
 O H:GLU215 2.3 69.3 1.0
OE2 H:GLU220 2.4 60.1 1.0
O H:ASP212 2.6 55.6 1.0
OE1 H:GLU210 2.6 54.7 1.0
OD1 H:ASP217 3.0 51.4 1.0
N H:ASP212 3.2 64.4 1.0
C H:ASP212 3.4 52.8 1.0
C H:GLU215 3.4 74.4 1.0
CB H:ASP212 3.5 53.0 1.0
CD H:GLU220 3.5 65.4 1.0
CA H:ASP212 3.6 60.4 1.0
CD H:GLU210 3.6 55.3 1.0
CG H:ASP217 3.7 56.1 1.0
OE2 H:GLU210 3.9 50.4 1.0
OD2 H:ASP217 4.0 51.5 1.0
N H:ASP217 4.2 63.9 1.0
N H:HIS211 4.2 63.6 1.0
CG H:GLU220 4.3 54.6 1.0
N H:HIS216 4.3 62.1 1.0
CA H:GLU215 4.4 74.0 1.0
C H:HIS211 4.4 60.0 1.0
CA H:HIS216 4.4 60.9 1.0
OE1 H:GLU220 4.4 70.9 1.0
N H:GLU215 4.5 60.5 1.0
CB H:GLU215 4.5 69.9 1.0
N H:LEU213 4.7 40.7 1.0
CA H:HIS211 4.8 53.6 1.0
C H:HIS216 4.8 55.1 1.0
CB H:ASP217 4.9 53.4 1.0
CG H:GLU215 4.9 59.3 1.0
CG H:ASP212 4.9 69.1 1.0
CG H:GLU210 5.0 53.1 1.0

Calcium binding site 5 out of 10 in 8cn9

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Calcium binding site 5 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca502

b:49.8
occ:1.00
 O H:SER339 2.3 59.6 1.0
OG H:SER339 2.7 69.7 1.0
OD1 H:ASP338 2.8 61.7 1.0
CA H:GLY365 2.8 66.0 1.0
C H:SER339 3.4 69.8 1.0
N H:GLY365 3.4 80.8 1.0
O H:GLY367 3.7 67.7 1.0
C H:GLY365 3.8 63.4 1.0
CB H:SER339 3.9 69.3 1.0
CG H:ASP338 3.9 80.1 1.0
CA H:SER339 4.0 66.4 1.0
N H:SER339 4.1 65.4 1.0
C H:TRP364 4.2 69.2 1.0
CA H:GLY375 4.2 53.0 1.0
N H:GLN366 4.4 50.5 1.0
O H:TRP364 4.4 65.6 1.0
OD2 H:ASP338 4.4 84.5 1.0
N H:CYS340 4.5 72.6 1.0
O H:GLY365 4.6 83.0 1.0
CA H:CYS340 4.8 68.1 1.0
C H:GLY367 4.8 96.8 1.0
N H:GLY367 4.9 90.8 1.0
O H:PHE374 4.9 79.7 1.0

Calcium binding site 6 out of 10 in 8cn9

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Calcium binding site 6 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca301

b:80.9
occ:1.00
 OD1 K:ASN138 2.3 53.0 1.0
O K:ALA112 2.4 84.4 1.0
CG K:ASN138 3.2 64.4 1.0
OG K:SER114 3.2 72.8 1.0
ND2 K:ASN138 3.4 57.5 1.0
C K:ALA112 3.6 66.4 1.0
C K:PRO113 3.9 73.3 1.0
O K:PRO113 4.0 93.9 1.0
N K:SER114 4.2 68.8 1.0
CA K:PRO113 4.2 63.3 1.0
N K:PRO113 4.4 53.9 1.0
CB K:SER114 4.4 63.0 1.0
CB K:ASN138 4.5 73.5 1.0
CA K:ALA112 4.6 66.5 1.0
O K:ASN138 4.7 92.4 1.0
CA K:SER114 4.7 72.2 1.0
CB K:ALA112 4.7 61.9 1.0
N K:ALA112 4.9 61.9 1.0

Calcium binding site 7 out of 10 in 8cn9

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Calcium binding site 7 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca501

b:52.9
occ:1.00
 O M:ASP212 2.2 68.1 1.0
OE2 M:GLU220 2.3 35.6 1.0
N M:ASP212 2.7 58.8 1.0
OE2 M:GLU210 2.9 48.7 1.0
C M:ASP212 3.0 55.0 1.0
O M:GLU215 3.2 56.8 1.0
N M:HIS211 3.2 62.3 1.0
CA M:ASP212 3.3 48.5 1.0
CD M:GLU210 3.4 60.7 1.0
CD M:GLU220 3.4 48.6 1.0
CG M:GLU210 3.5 49.9 1.0
C M:HIS211 3.7 67.1 1.0
OD1 M:ASP217 3.7 42.1 1.0
CB M:ASP212 3.7 47.3 1.0
CA M:HIS211 4.0 52.1 1.0
CA M:GLU210 4.0 55.2 1.0
C M:GLU210 4.1 53.4 1.0
N M:LEU213 4.1 48.5 1.0
CG M:GLU220 4.2 54.0 1.0
CB M:GLU210 4.3 57.7 1.0
OE1 M:GLU220 4.4 51.6 1.0
OE1 M:GLU210 4.4 67.7 1.0
C M:GLU215 4.4 50.9 1.0
CB M:HIS211 4.6 41.2 1.0
CG M:ASP217 4.6 47.8 1.0
CA M:LEU213 4.7 45.1 1.0
O M:HIS211 4.7 77.3 1.0
OD2 M:ASP217 4.9 51.0 1.0
CG M:ASP212 5.0 70.8 1.0

Calcium binding site 8 out of 10 in 8cn9

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Calcium binding site 8 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca502

b:57.1
occ:1.00
 O M:SER339 2.3 82.3 1.0
OG M:SER339 2.4 64.5 1.0
CA M:GLY365 2.8 84.4 1.0
N M:GLY365 2.9 79.9 1.0
C M:SER339 3.4 88.2 1.0
C M:TRP364 3.5 73.5 1.0
CB M:SER339 3.6 66.5 1.0
CG2 M:VAL362 3.9 50.5 1.0
O M:TRP364 3.9 85.0 1.0
CA M:SER339 4.0 72.8 1.0
OD1 M:ASP338 4.1 80.0 1.0
C M:GLY365 4.1 88.5 1.0
CA M:TRP364 4.3 73.0 1.0
O M:CYS340 4.4 73.2 1.0
N M:CYS340 4.4 91.4 1.0
CA M:GLY375 4.4 46.9 1.0
N M:SER339 4.4 80.8 1.0
CE1 M:TYR377 4.5 63.8 1.0
N M:TRP364 4.6 61.8 1.0
C M:CYS340 4.6 91.3 1.0
O M:GLY365 4.7 86.8 1.0
CA M:CYS340 4.7 94.7 1.0
O M:VAL376 4.8 48.9 1.0
CG M:ASP338 4.9 75.6 1.0
C M:GLY375 4.9 47.7 1.0
N M:VAL376 4.9 44.3 1.0
OD2 M:ASP338 5.0 75.9 1.0

Calcium binding site 9 out of 10 in 8cn9

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Calcium binding site 9 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca501

b:53.0
occ:1.00
 OE2 R:GLU220 2.3 41.1 1.0
OE1 R:GLU210 2.4 59.7 1.0
OD1 R:ASP217 2.5 73.8 1.0
O R:GLU215 2.6 74.5 1.0
O R:ASP212 3.0 61.8 1.0
CD R:GLU220 3.2 55.5 1.0
CG R:ASP217 3.4 63.5 1.0
N R:ASP212 3.5 47.4 1.0
CD R:GLU210 3.6 62.4 1.0
OD2 R:ASP217 3.7 67.5 1.0
C R:GLU215 3.8 69.3 1.0
CG R:GLU220 3.8 70.0 1.0
C R:ASP212 3.9 58.6 1.0
N R:ASP217 3.9 52.1 1.0
N R:HIS211 4.0 69.7 1.0
CA R:ASP212 4.0 52.9 1.0
CB R:ASP212 4.0 55.4 1.0
OE1 R:GLU220 4.1 67.5 1.0
OE2 R:GLU210 4.1 61.8 1.0
CA R:HIS216 4.4 63.2 1.0
N R:HIS216 4.5 67.9 1.0
C R:HIS211 4.5 56.7 1.0
CB R:ASP217 4.6 45.4 1.0
C R:HIS216 4.7 56.1 1.0
CA R:HIS211 4.7 61.7 1.0
CA R:GLU210 4.7 51.3 1.0
CG R:GLU210 4.8 60.7 1.0
CA R:GLU215 4.9 56.7 1.0
C R:GLU210 4.9 52.1 1.0
CA R:ASP217 4.9 53.6 1.0
NZ R:LYS161 4.9 51.0 1.0
CB R:HIS211 5.0 52.7 1.0

Calcium binding site 10 out of 10 in 8cn9

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Calcium binding site 10 out of 10 in the Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Factor VII Binding Fab of the Bispecific Antibody Hmb-001 in Complex with Factor VII within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca502

b:65.1
occ:1.00
 OG R:SER339 2.3 43.7 1.0
OD1 R:ASP338 2.4 45.3 1.0
O R:SER339 2.5 80.8 1.0
CA R:GLY365 2.7 62.0 1.0
C R:SER339 3.4 70.5 1.0
CB R:SER339 3.4 45.1 1.0
CA R:GLY375 3.4 58.7 1.0
N R:SER339 3.5 41.0 1.0
N R:GLY365 3.5 61.8 1.0
CG R:ASP338 3.5 62.8 1.0
CA R:SER339 3.6 48.9 1.0
C R:GLY365 3.9 86.7 1.0
OD2 R:ASP338 4.0 81.2 1.0
CE1 R:TYR377 4.0 55.5 1.0
O R:TRP364 4.1 76.1 1.0
C R:TRP364 4.1 69.8 1.0
C R:GLY375 4.2 47.4 1.0
N R:GLN366 4.4 58.2 1.0
N R:VAL376 4.5 36.3 1.0
N R:GLY375 4.6 52.7 1.0
OH R:TYR377 4.6 46.7 1.0
N R:CYS340 4.6 62.0 1.0
C R:ASP338 4.6 42.0 1.0
O R:GLY365 4.7 120.0 1.0
CB R:ASP338 4.7 48.9 1.0
CZ R:TYR377 4.8 50.7 1.0
CD1 R:TYR377 4.9 54.3 1.0
O R:GLY375 4.9 50.6 1.0
O R:PHE374 5.0 72.6 1.0

Reference:

P.S.Gandhi, M.Zivkovic, H.Oestergaard, A.C.Bonde, M.N.Loevgreen, G.Schluckebier, E.Johansson, C.J.Rea, B.Soerensen, R.E.Schutgens, R.T.Urbanus, J.H.Faber. A Bispecific Antibody Approach For the Potential Prophylactic Treatment of Inherited Bleeding Disorders Nat Cardiovasc Res 2023.
ISSN: ESSN 2731-0590
Page generated: Fri Jul 19 07:41:43 2024

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