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Calcium in PDB 9cln: Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution

Enzymatic activity of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution

All present enzymatic activity of Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution:
3.4.21.5;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution (pdb code 9cln). 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 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution, PDB code: 9cln:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 9cln

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Calcium binding site 1 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A 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 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca1001

b:13.5
occ:1.00
 OG1 K:THR425 2.0 67.5 1.0
N K:THR425 2.2 67.5 1.0
CB K:THR425 2.5 67.5 1.0
OE12 Z:CGU25 2.6 14.6 1.0
CA K:THR425 2.8 67.5 1.0
CD1 Z:CGU25 3.0 16.1 1.0
OE11 Z:CGU25 3.2 16.5 1.0
C K:GLU424 3.3 65.7 1.0
C K:THR425 3.5 67.5 1.0
O K:THR425 3.6 67.5 1.0
CA K:GLU424 3.7 65.7 1.0
CB K:GLU424 3.9 65.7 1.0
CG2 K:THR425 4.0 67.5 1.0
CG Z:CGU25 4.1 17.7 1.0
O K:GLU424 4.3 65.7 1.0
CD2 Z:CGU25 4.5 15.3 1.0
N K:LEU426 4.6 67.0 1.0
CG K:GLU424 4.7 65.7 1.0
OG1 J:THR270 4.8 76.3 1.0
OE21 Z:CGU25 4.9 16.1 1.0
OE22 Z:CGU25 4.9 22.3 1.0

Calcium binding site 2 out of 7 in 9cln

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Calcium binding site 2 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A 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 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca601

b:14.3
occ:1.00
 OE11 Z:CGU7 2.5 8.1 1.0
OE22 Z:CGU7 2.5 8.1 1.0
CD1 Z:CGU7 3.2 13.1 1.0
CD2 Z:CGU7 3.2 9.3 1.0
CG Z:CGU7 3.5 10.9 1.0
OE11 Z:CGU26 3.7 11.8 1.0
CD1 Z:CGU26 4.2 14.3 1.0
OE21 Z:CGU7 4.2 13.6 1.0
OE12 Z:CGU7 4.3 13.2 1.0
OE12 Z:CGU26 4.5 10.3 1.0
CA Z:CA602 4.9 9.4 1.0
CG Z:CGU26 4.9 13.6 1.0

Calcium binding site 3 out of 7 in 9cln

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Calcium binding site 3 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A 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 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca602

b:9.4
occ:1.00
 OE12 Z:CGU26 2.5 10.3 1.0
OE11 Z:CGU26 2.5 11.8 1.0
OE22 Z:CGU29 2.7 10.3 1.0
CD1 Z:CGU26 2.8 14.3 1.0
OE21 Z:CGU29 3.2 14.5 1.0
N Z:GLY11 3.3 61.8 1.0
CD2 Z:CGU29 3.3 12.2 1.0
OE11 Z:CGU7 3.6 8.1 1.0
CA Z:GLY11 3.7 61.8 1.0
OE22 Z:CGU16 3.9 9.0 1.0
OE21 Z:CGU16 4.0 4.8 1.0
O Z:ARG9 4.0 52.3 1.0
C Z:LYS10 4.2 56.1 1.0
CG Z:CGU26 4.3 13.6 1.0
CD2 Z:CGU16 4.4 8.4 1.0
CA Z:LYS10 4.5 56.1 1.0
CD1 Z:CGU7 4.5 13.1 1.0
CA Z:CA603 4.6 12.6 1.0
CA Z:CGU26 4.7 15.5 1.0
CG Z:CGU29 4.7 13.0 1.0
CB Z:CGU26 4.8 14.9 1.0
O Z:CGU6 4.9 15.4 1.0
CA Z:CA601 4.9 14.3 1.0

Calcium binding site 4 out of 7 in 9cln

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Calcium binding site 4 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A 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 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca603

b:12.6
occ:1.00
 OE22 Z:CGU16 2.3 9.0 1.0
OE22 Z:CGU26 2.4 10.6 1.0
OE12 Z:CGU16 2.4 12.4 1.0
N Z:ALA1 2.5 28.7 1.0
OE12 Z:CGU26 2.6 10.3 1.0
OE12 Z:CGU6 2.6 15.9 1.0
CD2 Z:CGU16 2.7 8.4 1.0
CD1 Z:CGU16 3.1 12.0 1.0
OE21 Z:CGU16 3.2 4.8 1.0
CA Z:CA604 3.3 12.1 1.0
CD2 Z:CGU26 3.3 11.2 1.0
CA Z:ALA1 3.4 28.7 1.0
CG Z:CGU16 3.4 7.4 1.0
CD1 Z:CGU26 3.6 14.3 1.0
CD1 Z:CGU6 3.9 17.6 1.0
CG Z:CGU26 4.0 13.6 1.0
OE21 Z:CGU26 4.1 14.4 1.0
OE11 Z:CGU16 4.2 12.7 1.0
NH2 Z:ARG15 4.2 84.0 1.0
CB Z:CGU16 4.2 11.1 1.0
C Z:ALA1 4.3 28.7 1.0
N Z:ASN2 4.4 40.0 1.0
CB Z:ALA1 4.5 28.7 1.0
OE11 Z:CGU6 4.5 22.5 1.0
CA Z:CA602 4.6 9.4 1.0
OE11 Z:CGU26 4.7 11.8 1.0
OE22 Z:CGU20 4.8 14.7 1.0
CB Z:CGU26 4.8 14.9 1.0
O Z:ASN2 4.9 40.0 1.0
O Z:CGU6 4.9 15.4 1.0
CG Z:CGU6 5.0 18.2 1.0
OE21 Z:CGU20 5.0 12.8 1.0

Calcium binding site 5 out of 7 in 9cln

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Calcium binding site 5 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A 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 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca604

b:12.1
occ:1.00
 OE12 Z:CGU16 2.4 12.4 1.0
OE12 Z:CGU6 2.4 15.9 1.0
OE21 Z:CGU20 2.5 12.8 1.0
N Z:ALA1 2.5 28.7 1.0
OE11 Z:CGU6 2.6 22.5 1.0
CD1 Z:CGU6 2.7 17.6 1.0
OE22 Z:CGU20 2.9 14.7 1.0
CD2 Z:CGU20 3.1 10.2 1.0
CD1 Z:CGU16 3.3 12.0 1.0
CA Z:CA603 3.3 12.6 1.0
N Z:ASN2 3.4 40.0 1.0
OE11 Z:CGU16 3.4 12.7 1.0
O Z:ASN2 3.7 40.0 1.0
CA Z:ALA1 3.8 28.7 1.0
OG1 Z:THR3 4.0 46.5 1.0
CG Z:CGU6 4.1 18.2 1.0
C Z:ALA1 4.1 28.7 1.0
C Z:ASN2 4.2 40.0 1.0
CB Z:CGU6 4.3 15.4 1.0
CA Z:ASN2 4.3 40.0 1.0
CA Z:CA605 4.4 19.1 1.0
OE22 Z:CGU16 4.5 9.0 1.0
CG Z:CGU20 4.6 13.1 1.0
CG Z:CGU16 4.6 7.4 1.0
CB Z:ALA1 4.7 28.7 1.0
CB Z:ASN2 4.9 40.0 1.0
OE22 Z:CGU26 4.9 10.6 1.0
CD2 Z:CGU16 4.9 8.4 1.0
CD2 Z:CGU6 4.9 19.5 1.0

Calcium binding site 6 out of 7 in 9cln

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Calcium binding site 6 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A 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 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca605

b:19.1
occ:1.00
 OE11 Z:CGU6 2.4 22.5 1.0
OE11 Z:CGU16 2.5 12.7 1.0
CD Z:ARG15 2.9 84.0 1.0
NE Z:ARG15 3.1 84.0 1.0
OE22 Z:CGU6 3.1 18.9 1.0
CG Z:ARG15 3.1 84.0 1.0
OE21 Z:CGU20 3.3 12.8 1.0
CD1 Z:CGU6 3.4 17.6 1.0
CZ Z:ARG15 3.5 84.0 1.0
CD1 Z:CGU16 3.7 12.0 1.0
NH1 Z:ARG15 3.7 84.0 1.0
CD2 Z:CGU6 3.9 19.5 1.0
OE12 Z:CGU6 4.2 15.9 1.0
CG Z:CGU6 4.3 18.2 1.0
CD2 Z:CGU20 4.4 10.2 1.0
NH2 Z:ARG15 4.4 84.0 1.0
OE12 Z:CGU16 4.4 12.4 1.0
CA Z:CA604 4.4 12.1 1.0
CB Z:ARG15 4.6 84.0 1.0
CG Z:CGU16 4.7 7.4 1.0
OE21 Z:CGU6 4.8 21.6 1.0
CG Z:CGU20 4.8 13.1 1.0

Calcium binding site 7 out of 7 in 9cln

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Calcium binding site 7 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of Human Adenovirus 5 (AD5)-Hexon-Fii Complex at 3.9A 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 5 (AD5)-Hexon-Fii Complex at 3.9A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca606

b:23.3
occ:1.00
 OE21 Z:CGU14 2.6 21.5 1.0
CD2 Z:CGU14 3.5 19.1 1.0
OE22 Z:CGU14 3.7 25.1 1.0
OE21 Z:CGU19 4.4 22.9 1.0
OE22 Z:CGU19 4.6 20.9 1.0
CD2 Z:CGU19 4.9 16.8 1.0
CG Z:CGU14 4.9 19.5 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 18:50:46 2024

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