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Calcium in PDB 1y10: Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State

Enzymatic activity of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State

All present enzymatic activity of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State:
4.6.1.1;

Protein crystallography data

The structure of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State, PDB code: 1y10 was solved by I.Tews, F.Findeisen, I.Sinning, A.Schultz, J.E.Schultz, J.U.Linder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.936, 146.830, 84.849, 90.00, 105.26, 90.00
R / Rfree (%) 19 / 24.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State (pdb code 1y10). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State, PDB code: 1y10:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1y10

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Calcium binding site 1 out of 8 in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:76.9
occ:1.00
 O A:LEU223 2.4 47.8 1.0
O A:HOH669 2.6 57.8 1.0
OD2 A:ASP265 2.8 60.8 1.0
OD2 A:ASP222 3.2 56.1 1.0
OD1 A:ASP265 3.2 57.7 1.0
CG A:ASP265 3.4 54.8 1.0
OD1 A:ASP222 3.4 56.2 1.0
C A:LEU223 3.6 46.0 1.0
CG A:ASP222 3.6 50.3 1.0
NH2 A:ARG298 3.7 70.8 1.0
CA A:VAL224 4.2 47.4 1.0
N A:GLY225 4.3 49.3 1.0
N A:VAL224 4.4 46.5 1.0
C A:VAL224 4.4 48.4 1.0
N A:LEU223 4.6 46.1 1.0
CA A:LEU223 4.7 46.4 1.0
CB A:ASP265 4.9 51.4 1.0
CZ A:ARG298 4.9 68.3 1.0
CA A:GLY225 5.0 49.5 1.0
C A:ASP222 5.0 46.4 1.0

Calcium binding site 2 out of 8 in 1y10

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Calcium binding site 2 out of 8 in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca608

b:70.3
occ:1.00
 O A:HOH673 2.5 55.5 1.0
OD1 B:ASP265 2.6 51.1 1.0
O B:HOH661 2.7 64.9 1.0
OE1 A:GLU136 2.9 53.9 1.0
OD2 B:ASP222 3.3 55.9 1.0
OE2 A:GLU136 3.3 58.1 1.0
CD A:GLU136 3.5 52.1 1.0
CG B:ASP265 3.7 51.5 1.0
CA B:CA606 4.0 62.8 1.0
OD2 B:ASP265 4.2 54.9 1.0
CG B:ASP222 4.5 52.5 1.0
CE1 A:HIS140 4.6 54.7 1.0
NE2 A:HIS140 4.6 50.9 1.0
CB B:ALA266 4.7 45.5 1.0
N B:ASP265 4.7 51.6 1.0
O B:ILE263 4.8 55.7 1.0
N B:ALA266 4.9 47.2 1.0

Calcium binding site 3 out of 8 in 1y10

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Calcium binding site 3 out of 8 in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca609

b:65.3
occ:1.00
 O A:HOH624 2.5 43.0 1.0
OE2 D:GLU44 2.8 55.9 1.0
OE1 A:GLU44 2.9 57.5 1.0
O A:HOH653 3.0 50.5 1.0
CD D:GLU44 3.7 56.9 1.0
O D:ASP63 3.8 47.9 1.0
CD A:GLU44 3.8 52.7 1.0
O A:HOH679 4.1 59.7 1.0
NE2 D:HIS58 4.2 63.9 1.0
NE2 A:HIS58 4.3 59.0 1.0
OE1 D:GLU44 4.3 60.0 1.0
OE2 A:GLU44 4.4 56.7 1.0
O A:ASP63 4.5 45.6 1.0
CG D:GLU44 4.5 49.6 1.0
CE1 A:HIS58 4.8 59.7 1.0
CG A:GLU44 4.8 54.0 1.0
C D:ASP63 4.8 45.6 1.0
CE1 D:HIS58 4.9 66.3 1.0
CD2 D:HIS58 4.9 64.1 1.0

Calcium binding site 4 out of 8 in 1y10

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Calcium binding site 4 out of 8 in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca606

b:62.8
occ:1.00
 O B:LEU223 2.3 47.8 1.0
O A:HOH673 2.5 55.5 1.0
OD2 B:ASP265 2.6 54.9 1.0
OD2 B:ASP222 3.0 55.9 1.0
OD1 B:ASP222 3.3 52.3 1.0
C B:LEU223 3.5 47.3 1.0
CG B:ASP265 3.5 51.5 1.0
CG B:ASP222 3.5 52.5 1.0
OD1 B:ASP265 3.7 51.1 1.0
CA A:CA608 4.0 70.3 1.0
CA B:VAL224 4.0 52.4 1.0
N B:VAL224 4.2 50.2 1.0
C B:VAL224 4.2 54.6 1.0
N B:GLY225 4.5 56.9 1.0
CA B:LEU223 4.5 47.0 1.0
N B:LEU223 4.6 46.2 1.0
O B:VAL224 4.6 54.0 1.0
OE1 A:GLU136 4.7 53.9 1.0
CB B:ASP265 4.9 51.1 1.0
CB B:ASP222 5.0 48.6 1.0

Calcium binding site 5 out of 8 in 1y10

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Calcium binding site 5 out of 8 in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:86.9
occ:1.00
 OD1 C:ASP265 2.8 55.2 1.0
O C:HOH690 2.8 49.0 1.0
OE2 D:GLU136 3.0 55.2 1.0
N C:ASP265 3.3 50.4 1.0
CG C:ASP265 3.6 52.2 1.0
OE1 D:GLU136 3.6 53.8 1.0
CD D:GLU136 3.7 51.4 1.0
CA C:GLY264 3.9 54.4 1.0
O C:ILE263 4.1 58.7 1.0
C C:GLY264 4.1 52.2 1.0
CB C:ASP265 4.2 49.1 1.0
CA C:ASP265 4.3 49.5 1.0
OD2 C:ASP265 4.3 49.5 1.0
NE2 D:HIS140 4.5 53.6 1.0
C C:ILE263 4.7 56.4 1.0
N C:GLY264 4.7 55.3 1.0
N C:ALA266 4.8 45.9 1.0
C C:ASP265 4.9 47.3 1.0
OD2 C:ASP222 4.9 54.2 1.0

Calcium binding site 6 out of 8 in 1y10

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Calcium binding site 6 out of 8 in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca605

b:85.4
occ:1.00
 O D:LEU223 2.5 52.7 1.0
OD2 D:ASP265 2.7 57.1 1.0
OD1 D:ASP222 2.9 62.0 1.0
CG D:ASP265 3.6 54.9 1.0
CG D:ASP222 3.6 53.8 1.0
C D:LEU223 3.7 52.6 1.0
OD2 D:ASP222 3.7 62.2 1.0
OD1 D:ASP265 3.8 55.2 1.0
C D:VAL224 4.2 58.7 1.0
CA D:VAL224 4.2 56.8 1.0
N D:GLY225 4.2 60.5 1.0
NH1 D:ARG298 4.3 68.1 1.0
N D:VAL224 4.4 54.9 1.0
O D:VAL224 4.6 59.1 1.0
N D:LEU223 4.7 49.2 1.0
CA D:LEU223 4.8 50.9 1.0
NH2 D:ARG298 4.9 66.0 1.0
CB D:ASP265 5.0 52.0 1.0

Calcium binding site 7 out of 8 in 1y10

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Calcium binding site 7 out of 8 in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca610

b:64.0
occ:1.00
 O C:HOH708 2.7 64.1 1.0
OE2 D:GLU195 3.2 48.5 1.0
O C:HOH682 3.6 53.9 1.0
OE1 D:GLU195 3.9 44.9 1.0
CD D:GLU195 4.0 45.8 1.0
N C:ASN49 4.0 45.6 1.0
CG1 D:VAL307 4.2 49.7 1.0
O C:ASN49 4.2 44.9 1.0
O C:ALA47 4.2 45.8 1.0
CA C:THR48 4.5 45.4 1.0
C C:ASN49 4.8 45.8 1.0
C C:THR48 4.8 45.3 1.0
CG2 D:VAL199 4.9 40.7 1.0
CA C:ASN49 4.9 45.7 1.0
CG2 C:THR48 4.9 45.9 1.0

Calcium binding site 8 out of 8 in 1y10

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Calcium binding site 8 out of 8 in the Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Mycobacterial Adenylyl Cyclase RV1264, Holoenzyme, Inhibited State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca611

b:70.5
occ:1.00
 OD1 D:ASN319 3.6 49.7 1.0
CG D:ASN319 3.7 49.6 1.0
ND2 D:ASN319 3.7 51.3 1.0
NH2 C:ARG146 3.7 54.5 1.0
CG2 D:THR196 3.9 41.5 1.0
CZ C:ARG146 3.9 54.1 1.0
O D:HOH720 4.2 59.1 1.0
NE C:ARG146 4.3 53.5 1.0
NH1 C:ARG146 4.3 55.3 1.0
CB D:ASN319 4.5 50.1 1.0
O C:HOH636 4.9 55.6 1.0
O D:HOH649 5.0 43.4 1.0

Reference:

I.Tews, F.Findeisen, I.Sinning, A.Schultz, J.E.Schultz, J.U.Linder. The Structure of A pH-Sensing Mycobacterial Adenylyl Cyclase Holoenzyme Science V. 308 1020 2005.
ISSN: ISSN 0036-8075
PubMed: 15890882
DOI: 10.1126/SCIENCE.1107642
Page generated: Sat Dec 12 03:27:51 2020

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