Calcium in PDB 9cm9: Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A Resolution

Enzymatic activity of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A Resolution

All present enzymatic activity of Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A Resolution:
3.4.21.6;

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A Resolution (pdb code 9cm9). 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 AD657-Hexon-Fx Complex at 3.86A Resolution, PDB code: 9cm9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 9cm9

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Calcium binding site 1 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A 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 AD657-Hexon-Fx Complex at 3.86A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca501

b:13.5
occ:1.00
 OE21 Z:CGU25 2.5 16.1 1.0
NH2 Z:ARG28 2.5 22.4 1.0
CB L:THR431 2.8 89.8 1.0
CD2 Z:CGU25 2.8 15.3 1.0
OG1 L:THR431 3.0 89.8 1.0
OE12 Z:CGU29 3.2 17.4 1.0
N L:THR431 3.3 89.8 1.0
CG Z:CGU25 3.5 17.7 1.0
OE22 Z:CGU25 3.5 22.3 1.0
CA L:THR431 3.5 89.8 1.0
CZ Z:ARG28 3.8 23.5 1.0
CD1 Z:CGU25 3.8 16.1 1.0
O L:THR431 3.9 89.8 1.0
CG2 L:THR431 4.0 89.8 1.0
OE11 Z:CGU25 4.0 16.5 1.0
C L:THR431 4.1 89.8 1.0
NH2 L:ARG456 4.3 88.0 1.0
NE Z:ARG28 4.4 23.2 1.0
C L:ASP430 4.4 86.6 1.0
OE12 Z:CGU25 4.4 14.6 1.0
CD1 Z:CGU29 4.5 16.8 1.0
OG K:SER276 4.6 83.9 1.0
CB K:SER276 4.7 83.9 1.0
NH1 Z:ARG28 4.7 21.4 1.0
CA L:ASP430 4.8 86.6 1.0
OE22 Z:CGU29 4.9 10.3 1.0
CA Z:CA502 4.9 14.3 1.0
CB Z:CGU25 4.9 13.2 1.0

Calcium binding site 2 out of 7 in 9cm9

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Calcium binding site 2 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A 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 AD657-Hexon-Fx Complex at 3.86A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca502

b:14.3
occ:1.00
 OE22 Z:CGU7 2.7 8.1 1.0
OE21 Z:CGU7 3.2 13.6 1.0
CD2 Z:CGU7 3.3 9.3 1.0
OE22 Z:CGU29 3.3 10.3 1.0
OE12 Z:CGU29 3.4 17.4 1.0
OE11 Z:CGU25 3.4 16.5 1.0
CD1 Z:CGU29 3.6 16.8 1.0
CD2 Z:CGU29 3.7 12.2 1.0
OE11 Z:CGU29 3.8 20.6 1.0
O L:THR429 3.9 86.6 1.0
OE21 Z:CGU29 4.3 14.5 1.0
CG Z:CGU29 4.3 13.0 1.0
CD1 Z:CGU25 4.5 16.1 1.0
CA L:ASP430 4.6 86.6 1.0
C L:THR429 4.7 86.6 1.0
CG Z:CGU7 4.8 10.9 1.0
CA Z:CA501 4.9 13.5 1.0
CG Z:CGU25 5.0 17.7 1.0
N L:THR431 5.0 89.8 1.0

Calcium binding site 3 out of 7 in 9cm9

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Calcium binding site 3 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A 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 AD657-Hexon-Fx Complex at 3.86A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca503

b:9.4
occ:1.00
 CA Z:CA504 2.1 12.6 1.0
OE21 Z:CGU29 2.4 14.5 1.0
N Z:GLY11 2.4 17.2 1.0
OE12 Z:CGU7 2.6 13.2 1.0
CA Z:GLY11 3.0 17.8 1.0
C Z:LYS10 3.3 18.4 1.0
CD2 Z:CGU29 3.6 12.2 1.0
CA Z:LYS10 3.6 19.3 1.0
CD1 Z:CGU7 3.6 13.1 1.0
CB Z:CGU29 4.0 11.0 1.0
OE11 Z:CGU7 4.1 8.1 1.0
O Z:LYS10 4.2 18.3 1.0
CG Z:CGU29 4.4 13.0 1.0
N Z:LYS10 4.5 17.4 1.0
C Z:GLY11 4.5 16.6 1.0
OE22 Z:CGU29 4.5 10.3 1.0
CD2 Z:CGU7 4.5 9.3 1.0
O Z:LYS9 4.6 20.5 1.0
OE22 Z:CGU16 4.6 9.0 1.0
OE21 Z:CGU7 4.7 13.6 1.0
CG Z:CGU7 4.7 10.9 1.0
CA Z:CGU26 4.7 15.5 1.0
CB Z:LYS10 4.8 30.0 1.0
OE22 Z:CGU7 4.8 8.1 1.0
CB Z:CGU26 4.8 14.9 1.0
C Z:LYS9 4.8 15.4 1.0
OE21 Z:CGU16 4.9 4.8 1.0

Calcium binding site 4 out of 7 in 9cm9

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Calcium binding site 4 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A 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 AD657-Hexon-Fx Complex at 3.86A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca504

b:12.6
occ:1.00
 CA Z:CA503 2.1 9.4 1.0
OE21 Z:CGU29 2.4 14.5 1.0
OE12 Z:CGU7 2.5 13.2 1.0
OE11 Z:CGU7 2.8 8.1 1.0
CB Z:CGU26 2.8 14.9 1.0
CD1 Z:CGU7 2.9 13.1 1.0
OE22 Z:CGU16 3.0 9.0 1.0
CA Z:CGU26 3.1 15.5 1.0
CA Z:GLY11 3.5 17.8 1.0
CD2 Z:CGU29 3.6 12.2 1.0
N Z:GLY11 3.7 17.2 1.0
O Z:CGU26 3.8 17.8 1.0
CD2 Z:CGU16 4.0 8.4 1.0
C Z:CGU26 4.0 16.6 1.0
OE12 Z:CGU26 4.0 10.3 1.0
OE22 Z:CGU29 4.1 10.3 1.0
OE21 Z:CGU16 4.1 4.8 1.0
CG Z:CGU7 4.1 10.9 1.0
CG Z:CGU26 4.2 13.6 1.0
N Z:CGU26 4.3 18.7 1.0
CD2 Z:CGU7 4.4 9.3 1.0
OE22 Z:CGU7 4.4 8.1 1.0
CD1 Z:CGU26 4.5 14.3 1.0
C Z:LYS10 4.7 18.4 1.0
OE22 Z:CGU26 4.7 10.6 1.0
OE12 Z:CGU6 4.8 15.9 1.0
CG Z:CGU29 4.8 13.0 1.0
CB Z:CGU29 4.8 11.0 1.0
C Z:GLY11 4.9 16.6 1.0
CD2 Z:CGU26 5.0 11.2 1.0

Calcium binding site 5 out of 7 in 9cm9

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Calcium binding site 5 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A 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 AD657-Hexon-Fx Complex at 3.86A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca505

b:12.1
occ:1.00
 NE Z:ARG15 2.4 8.2 1.0
OE11 Z:CGU16 2.4 12.7 1.0
OE21 Z:CGU16 2.5 4.8 1.0
CZ Z:ARG15 2.9 9.3 1.0
CG Z:CGU16 2.9 7.4 1.0
CD1 Z:CGU16 2.9 12.0 1.0
CD2 Z:CGU16 3.0 8.4 1.0
CD Z:ARG15 3.0 2.0 1.0
NH2 Z:ARG15 3.2 6.2 1.0
OE12 Z:CGU6 3.2 15.9 1.0
CG Z:ARG15 3.4 4.3 1.0
CG Z:CGU6 3.6 18.2 1.0
NH1 Z:ARG15 3.7 6.5 1.0
CD1 Z:CGU6 3.9 17.6 1.0
CD2 Z:CGU6 3.9 19.5 1.0
OE22 Z:CGU6 4.0 18.9 1.0
OE12 Z:CGU16 4.1 12.4 1.0
OE22 Z:CGU16 4.2 9.0 1.0
CB Z:CGU16 4.4 11.1 1.0
CB Z:ARG15 4.5 5.1 1.0
OE21 Z:CGU6 4.7 21.6 1.0
N Z:CGU16 4.8 11.8 1.0
CB Z:CGU6 4.9 15.4 1.0
CA Z:CGU16 4.9 12.2 1.0
CA Z:CA506 5.0 19.1 1.0

Calcium binding site 6 out of 7 in 9cm9

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Calcium binding site 6 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A 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 AD657-Hexon-Fx Complex at 3.86A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca506

b:19.1
occ:1.00
 OE21 Z:CGU20 2.4 12.8 1.0
OE11 Z:CGU16 3.3 12.7 1.0
CD2 Z:CGU20 3.5 10.2 1.0
CG Z:CGU20 4.0 13.1 1.0
OE22 Z:CGU6 4.1 18.9 1.0
CD1 Z:CGU16 4.3 12.0 1.0
N Z:ALA1 4.4 4.1 1.0
OE21 Z:CGU6 4.4 21.6 1.0
CD1 Z:CGU20 4.5 12.7 1.0
OE22 Z:CGU20 4.6 14.7 1.0
CD2 Z:CGU6 4.6 19.5 1.0
OE12 Z:CGU20 4.6 19.0 1.0
OE12 Z:CGU16 4.7 12.4 1.0
O Z:ARG15 4.7 10.5 1.0
CA Z:CA505 5.0 12.1 1.0

Calcium binding site 7 out of 7 in 9cm9

Go back to Calcium Binding Sites List in 9cm9
Calcium binding site 7 out of 7 in the Cryo-Em Model Derived From Localized Reconstruction of AD657-Hexon-Fx Complex at 3.86A 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 AD657-Hexon-Fx Complex at 3.86A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Ca507

b:23.3
occ:1.00
 OE12 Z:CGU19 2.5 20.5 1.0
OE12 Z:CGU14 2.5 17.1 1.0
CD1 Z:CGU14 3.3 13.0 1.0
SD Z:MET18 3.7 30.0 1.0
CD1 Z:CGU19 3.7 17.4 1.0
CG Z:CGU14 3.7 19.5 1.0
OE11 Z:CGU14 4.2 13.5 1.0
OE22 Z:CGU14 4.3 25.1 1.0
OE22 Z:CGU19 4.3 20.9 1.0
CE Z:MET18 4.4 30.0 1.0
OE11 Z:CGU19 4.5 15.2 1.0
CD2 Z:CGU14 4.5 19.1 1.0
CG Z:CGU19 4.7 19.9 1.0
O Z:CGU14 4.8 18.0 1.0
CB Z:CGU14 4.9 15.4 1.0
CD2 Z:CGU19 5.0 16.8 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 18:50:58 2024

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