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Calcium in PDB 9cli: Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution

Enzymatic activity of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution

All present enzymatic activity of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution:
3.4.21.6;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution (pdb code 9cli). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution, PDB code: 9cli:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 9cli

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Calcium binding site 1 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1001

b:13.5
occ:1.00
 OE11 Z:CGU25 2.6 16.5 1.0
OG1 L:THR425 2.6 72.2 1.0
CB L:THR425 2.8 72.2 1.0
N L:THR425 3.4 72.2 1.0
CD1 Z:CGU25 3.5 16.1 1.0
OE12 Z:CGU29 3.6 17.4 1.0
CA L:THR425 3.7 72.2 1.0
CG Z:CGU25 3.7 17.7 1.0
CD2 Z:CGU25 4.0 15.3 1.0
OE21 Z:CGU25 4.0 16.1 1.0
CG2 L:THR425 4.0 72.2 1.0
O L:THR425 4.2 72.2 1.0
CA Z:CA501 4.3 14.3 1.0
C L:THR425 4.3 72.2 1.0
C L:GLU424 4.6 69.9 1.0
OE12 Z:CGU25 4.6 14.6 1.0
CD1 Z:CGU29 4.7 16.8 1.0
OE22 Z:CGU25 4.8 22.3 1.0
CA L:GLU424 4.9 69.9 1.0

Calcium binding site 2 out of 7 in 9cli

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Calcium binding site 2 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca501

b:14.3
occ:1.00
 OE12 Z:CGU29 2.5 17.4 1.0
OE22 Z:CGU29 2.5 10.3 1.0
OE12 Z:CGU7 2.9 13.2 1.0
OE22 Z:CGU7 3.3 8.1 1.0
CD1 Z:CGU29 3.4 16.8 1.0
CD2 Z:CGU29 3.5 12.2 1.0
CD1 Z:CGU7 3.6 13.1 1.0
CD2 Z:CGU7 4.0 9.3 1.0
CG Z:CGU29 4.0 13.0 1.0
OE11 Z:CGU7 4.1 8.1 1.0
OE11 Z:CGU29 4.3 20.6 1.0
CA L:CA1001 4.3 13.5 1.0
O L:THR423 4.4 66.6 1.0
OE21 Z:CGU29 4.4 14.5 1.0
CG Z:CGU7 4.4 10.9 1.0
OE21 Z:CGU7 4.7 13.6 1.0
OE11 Z:CGU25 4.8 16.5 1.0
CG Z:CGU25 4.9 17.7 1.0
CA L:GLU424 5.0 69.9 1.0

Calcium binding site 3 out of 7 in 9cli

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Calcium binding site 3 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca502

b:9.4
occ:1.00
 CA Z:CA503 2.0 12.6 1.0
OE22 Z:CGU16 2.5 9.0 1.0
OE21 Z:CGU29 2.6 14.5 1.0
CA Z:GLY11 2.9 17.8 1.0
CG2 Z:VAL30 3.0 9.3 1.0
CA Z:CGU26 3.2 15.5 1.0
C Z:GLY11 3.3 16.6 1.0
CB Z:CGU26 3.6 14.9 1.0
O Z:CGU26 3.6 17.8 1.0
CD2 Z:CGU16 3.6 8.4 1.0
N Z:HIS12 3.7 14.9 1.0
OE12 Z:CGU26 3.7 10.3 1.0
CB Z:CGU29 3.7 11.0 1.0
CD2 Z:CGU29 3.7 12.2 1.0
C Z:CGU26 3.8 16.6 1.0
O Z:GLY11 3.9 19.0 1.0
N Z:GLY11 4.0 17.2 1.0
OE12 Z:CGU16 4.1 12.4 1.0
N Z:VAL30 4.2 16.5 1.0
O Z:CGU25 4.2 20.8 1.0
OE21 Z:CGU16 4.2 4.8 1.0
N Z:CGU26 4.3 18.7 1.0
CG Z:CGU29 4.4 13.0 1.0
OE11 Z:CGU7 4.4 8.1 1.0
CB Z:VAL30 4.5 15.8 1.0
CD1 Z:CGU26 4.6 14.3 1.0
CA Z:HIS12 4.6 13.2 1.0
C Z:HIS12 4.7 13.7 1.0
CG Z:CGU16 4.7 7.4 1.0
O Z:HIS12 4.7 12.5 1.0
C Z:CGU25 4.7 16.8 1.0
CG Z:CGU26 4.7 13.6 1.0
CA Z:CGU29 4.7 13.8 1.0
OE22 Z:CGU29 4.7 10.3 1.0
CB Z:CGU16 4.8 11.1 1.0
CD1 Z:CGU16 4.9 12.0 1.0
CA Z:VAL30 4.9 16.6 1.0
C Z:CGU29 4.9 16.1 1.0
N Z:CGU29 4.9 14.6 1.0

Calcium binding site 4 out of 7 in 9cli

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Calcium binding site 4 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca503

b:12.6
occ:1.00
 CA Z:CA502 2.0 9.4 1.0
OE22 Z:CGU16 2.4 9.0 1.0
OE12 Z:CGU16 2.4 12.4 1.0
OE12 Z:CGU26 2.5 10.3 1.0
OE21 Z:CGU29 2.7 14.5 1.0
CD2 Z:CGU16 2.9 8.4 1.0
CA Z:GLY11 3.0 17.8 1.0
CB Z:CGU26 3.3 14.9 1.0
OE11 Z:CGU7 3.3 8.1 1.0
CD1 Z:CGU26 3.3 14.3 1.0
CD1 Z:CGU16 3.4 12.0 1.0
OE21 Z:CGU16 3.5 4.8 1.0
CA Z:CGU26 3.6 15.5 1.0
CG Z:CGU16 3.8 7.4 1.0
CG Z:CGU26 3.9 13.6 1.0
CD2 Z:CGU29 3.9 12.2 1.0
N Z:GLY11 3.9 17.2 1.0
C Z:GLY11 4.0 16.6 1.0
OE11 Z:CGU26 4.2 11.8 1.0
CD1 Z:CGU7 4.2 13.1 1.0
CG Z:CGU7 4.3 10.9 1.0
N Z:HIS12 4.3 14.9 1.0
CB Z:CGU16 4.4 11.1 1.0
OE22 Z:CGU29 4.5 10.3 1.0
N Z:CGU26 4.6 18.7 1.0
OE11 Z:CGU16 4.6 12.7 1.0
OE11 Z:CGU6 4.7 22.5 1.0
C Z:CGU26 4.8 16.6 1.0
CA Z:CGU7 4.8 13.4 1.0
O Z:CGU26 4.8 17.8 1.0
CD2 Z:CGU26 4.9 11.2 1.0
OE22 Z:CGU26 4.9 10.6 1.0
O Z:GLY11 4.9 19.0 1.0
CG2 Z:VAL30 4.9 9.3 1.0

Calcium binding site 5 out of 7 in 9cli

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Calcium binding site 5 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca504

b:12.1
occ:1.00
 O Z:ARG15 2.4 10.5 1.0
OE21 Z:CGU16 2.4 4.8 1.0
OE12 Z:CGU6 2.4 15.9 1.0
OE11 Z:CGU6 2.8 22.5 1.0
C Z:ARG15 2.9 10.5 1.0
CB Z:ARG15 2.9 5.1 1.0
CG Z:CGU16 2.9 7.4 1.0
CD1 Z:CGU6 2.9 17.6 1.0
CD2 Z:CGU16 3.0 8.4 1.0
CA Z:ARG15 3.5 11.2 1.0
N Z:CGU16 3.7 11.8 1.0
CD1 Z:CGU16 3.8 12.0 1.0
CB Z:CGU16 4.1 11.1 1.0
CA Z:CGU16 4.1 12.2 1.0
OE22 Z:CGU16 4.2 9.0 1.0
CG Z:ARG15 4.2 4.3 1.0
OE11 Z:CGU16 4.2 12.7 1.0
O Z:HIS12 4.4 12.5 1.0
CG Z:CGU6 4.4 18.2 1.0
CD Z:ARG15 4.5 2.0 1.0
N Z:ARG15 4.6 13.6 1.0
OE12 Z:CGU16 4.6 12.4 1.0
N Z:HIS12 4.6 14.9 1.0
OE21 Z:CGU20 4.7 12.8 1.0
OE22 Z:CGU20 4.9 14.7 1.0

Calcium binding site 6 out of 7 in 9cli

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Calcium binding site 6 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca505

b:19.1
occ:1.00
 OE21 Z:CGU6 4.9 21.6 1.0

Calcium binding site 7 out of 7 in 9cli

Go back to Calcium Binding Sites List in 9cli
Calcium binding site 7 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus (AD5)-Hexon-Fx Complex at 3.6A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca506

b:23.3
occ:1.00
 SD Z:MET18 2.8 30.0 1.0
OE22 Z:CGU14 3.3 25.1 1.0
CE Z:MET18 3.6 30.0 1.0
CD2 Z:CGU14 4.1 19.1 1.0
CG Z:CGU14 4.3 19.5 1.0
CG Z:MET18 4.5 30.0 1.0
OE12 Z:CGU19 4.7 20.5 1.0
CD1 Z:CGU14 4.7 13.0 1.0
O Z:CGU14 4.8 18.0 1.0
OE12 Z:CGU14 4.9 17.1 1.0

Reference:

H.E.Mudrick, S.C.Lu, J.Bhandari, M.E.Barry, J.R.Hemsath, F.G.M.Andres, O.X.Ma, M.A.Barry, V.S.Reddy. Structure-Derived Insights From Blood Factors Binding to the Surfaces of Different Adenoviruses. Nat Commun V. 15 9768 2024.
ISSN: ESSN 2041-1723
PubMed: 39528527
DOI: 10.1038/S41467-024-54049-9
Page generated: Tue Dec 10 18:50:57 2024

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